Last updated: 2025-07-22

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Introduction

Here in this document we present figures, tables, and statistics for the phasing evaluation on the autosomes. This sample consists of 602 individuals phased using a reference panel of unrelated individuals from the 1000 genomes project. The phasing results are compared to a pedigree-adjusted phased genome for each sample.

Libraries and Data

library(tidyverse)
library(pander)
library(reactable)
library(yaml)
library(gtsummary)

library(grid)
library(gridExtra) 

config_obj <- yaml::read_yaml("_config.yaml")

cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")

df_subj <- read_csv("data/1kgp/subject_info.csv")
ped_df <- read_table("data/1kgp/1kGP.3202_samples.pedigree_info.txt")

child_ids <- ped_df %>% filter(fatherID != "0" & motherID != "0") %>% pull(sampleID)
unrel_ids <- scan("data/1kgp/unrelated_subjects.txt", what = character())

df_subj_rel <- df_subj %>%
  filter(SAMPLE_NAME %in% child_ids)
df_subj_rel$id2 <- 1:602

df_subj_unrel <- df_subj %>%
  filter(SAMPLE_NAME %in% unrel_ids)

Switch Error Summaries

df_switch_trio <- vector(mode = "list", length = 22)


for(i in 1:22){
  df_switch_trio[[i]] <- read_csv(paste0(config_obj$base_dir, "/output/trio_phase_", i, "/switch_errors/summary.csv"),
                                  show_col_types = FALSE)
}

And let’s also load the results from when we phase without the triple heterozygous positions:

df_switch_trio_noth <- read_csv("output/all_noTH.csv", show_col_types = F)

Heterozygous Position Counts

# het dfs
df_het <- vector(mode = "list", length = 22)

for(i in 1:22){
  df_het[[i]] <- read_tsv(paste0(config_obj$base_dir, "/output/trio_phase_", i, "/no_th/het_pos_count.tsv"),
                   col_names = c("id", "n_het"), 
                   show_col_types = FALSE)
}

deCODE genetic maps (cM/MB)

df_decode <- vector(mode = "list", length = 22)

for(i in 1:22){
  df_decode[[i]] <- read_tsv(paste0("data/decode/chr", i, "_recomb.bed"), col_names = c("chr", "start", "end", "cM_MB"), show_col_types = FALSE)
}

Chr X Results

We’ll also pull in the results on chromosome X for the synthetic diploids to allow for comparisons of rates between 15 and X.

sd_pair_info_df <- read_delim("data/sample_pairs.csv", col_names = c("POP", "ID1", "ID2"))
Rows: 1000 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (3): POP, ID1, ID2

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
sd_pair_info_df <- left_join(sd_pair_info_df, df_subj, by = c("ID1"="SAMPLE_NAME")) %>%
  rename(SP = SUPER) %>%
  select(-POPULATION)

df_switch_x <- read_csv(paste0(config_obj$base_dir,"/output/switch_errors/switch_errors/summary.csv"))
Rows: 1000 Columns: 45
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr  (2): pop, subpop
dbl (43): pair_id, n_switch_eagle, n_switch_beagle, n_switch_shapeit, n_flip...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
df_het_x <- read_tsv(paste0(config_obj$base_dir, "/output/switch_errors/het_pos_count.tsv"), col_names = c("id", "n_het"))
Rows: 1000 Columns: 2
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
dbl (2): id, n_het

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
n_var_site_x <- 1722954
df_het_x$frac_het <- df_het_x$n_het / n_var_site_x

sd_pair_info_df$n_het <-df_het_x$n_het
sd_pair_info_df$frac_het <-df_het_x$frac_het

df_decode_x <- read_tsv("data/decode/chrX_recomb.bed", col_names = c("chr", "start", "end", "cM_MB"))
Rows: 23976 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (1): chr
dbl (3): start, end, cM_MB

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Subject Information

The 1000 Genomes collection of 3,202 genomes is sampled from 26 different populations, each belonging to 1 of 5 distinct super-populations (AFR, AMR, EAS, EUR, SAS). All 26 populations are represented in the 2,504 1kGP phase 3 subjects, but not all are present in the 602 trios sequenced by the New York Genome Center:

df_subj %>%
  group_by(SUPER, POPULATION) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("SUPER"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)
`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.
df_subj_rel %>%
  group_by(SUPER, POPULATION) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("SUPER"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)
`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.
df_subj_unrel %>%
  group_by(SUPER, POPULATION) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("SUPER"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)
`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.

For completeness, we also tabulate other summary information about the 602 trios (which is just sex; 1 - male, 2 - female):

df_subj_rel %>%
  group_by(sex) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("sex"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)
df_subj_unrel %>%
  group_by(sex) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("sex"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)

All Autosome Summaries

Total Errors

First let’s get an overall error rate across all 22 autosomes based on our re-phasing of the trio probands:

df_total <- df_switch_trio[[1]] %>%
  mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
         Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
         SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
  mutate(chrom = 1)

df_total_noth <- df_switch_trio_noth %>%
  mutate(Eagle = (n_switch_e + n_flip_e) / n_het,
         Beagle = (n_switch_b + n_flip_b) / n_het,
         SHAPEIT = (n_switch_s + n_flip_s) / n_het) %>%
  select(Eagle, Beagle, SHAPEIT, sample, chrom)

df_total_noth <- df_total_noth %>%
  left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
  rename(pair_id = sample) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)

for(i in 2:22){
  df_total <- bind_rows(df_total, 
                        {
                          df_switch_trio[[i]] %>%
                            mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
                                   Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
                            mutate(chrom = i)
                        })
}

df_total <- df_total %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
                                   Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

df_total_noth <- df_total_noth %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
                                   Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

Total Error Rates: with TH

df_total %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  knitr::kable()
chrom Beagle Eagle SHAPEIT
1 0.0067395 0.0067223 0.0071348
2 0.0067182 0.0066709 0.0071241
3 0.0062862 0.0062368 0.0066700
4 0.0058272 0.0058086 0.0061830
5 0.0062772 0.0062116 0.0066640
6 0.0056205 0.0056106 0.0059695
7 0.0066444 0.0066400 0.0070178
8 0.0016721 0.0022869 0.0017815
9 0.0079744 0.0079202 0.0083190
10 0.0064289 0.0064593 0.0068026
11 0.0063130 0.0062888 0.0066795
12 0.0064549 0.0064011 0.0068462
13 0.0062073 0.0061843 0.0065682
14 0.0069985 0.0070401 0.0074116
15 0.0080919 0.0081443 0.0085070
16 0.0080883 0.0081102 0.0085211
17 0.0082995 0.0083780 0.0086566
18 0.0066549 0.0066279 0.0070294
19 0.0077351 0.0078323 0.0080561
20 0.0080259 0.0080467 0.0083414
21 0.0086549 0.0088189 0.0090797
22 0.0098210 0.0100373 0.0101722
23 0.0030794 0.0036645 0.0031251
df_total %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable()
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
chrom SUPER Beagle Eagle SHAPEIT
1 AFR 0.0055470 0.0052014 0.0058600
1 AMR 0.0064375 0.0065297 0.0068945
1 EAS 0.0092799 0.0096876 0.0097752
1 EUR 0.0062678 0.0063948 0.0065600
1 SAS 0.0084880 0.0085297 0.0090237
2 AFR 0.0054907 0.0051472 0.0058282
2 AMR 0.0066014 0.0066504 0.0070537
2 EAS 0.0092474 0.0095998 0.0098008
2 EUR 0.0060698 0.0061718 0.0063560
2 SAS 0.0084829 0.0084545 0.0090015
3 AFR 0.0051191 0.0047501 0.0054396
3 AMR 0.0060628 0.0061345 0.0065287
3 EAS 0.0087136 0.0090203 0.0091782
3 EUR 0.0058531 0.0059451 0.0060974
3 SAS 0.0078949 0.0079269 0.0084038
4 AFR 0.0047064 0.0043872 0.0049933
4 AMR 0.0058144 0.0058702 0.0062470
4 EAS 0.0078453 0.0082126 0.0082989
4 EUR 0.0053370 0.0054733 0.0055894
4 SAS 0.0074061 0.0074566 0.0078482
5 AFR 0.0051628 0.0047968 0.0055004
5 AMR 0.0060247 0.0060731 0.0064754
5 EAS 0.0086690 0.0089300 0.0091428
5 EUR 0.0057598 0.0058361 0.0060024
5 SAS 0.0079450 0.0079505 0.0084528
6 AFR 0.0046691 0.0044083 0.0049870
6 AMR 0.0054834 0.0055737 0.0058509
6 EAS 0.0076252 0.0079459 0.0080756
6 EUR 0.0050195 0.0050966 0.0052602
6 SAS 0.0071493 0.0071820 0.0075932
7 AFR 0.0056451 0.0053659 0.0059259
7 AMR 0.0063283 0.0064342 0.0068119
7 EAS 0.0089896 0.0092754 0.0094416
7 EUR 0.0060694 0.0061896 0.0063094
7 SAS 0.0082539 0.0083194 0.0087699
8 AFR 0.0017555 0.0020756 0.0018302
8 AMR 0.0023261 0.0029894 0.0024296
8 EAS 0.0007489 0.0019593 0.0007036
8 EUR 0.0011225 0.0018524 0.0012282
8 SAS 0.0018944 0.0024787 0.0022310
9 AFR 0.0068396 0.0064942 0.0071230
9 AMR 0.0075185 0.0075597 0.0079218
9 EAS 0.0107378 0.0110860 0.0111549
9 EUR 0.0074135 0.0075191 0.0076602
9 SAS 0.0097581 0.0096966 0.0102146
10 AFR 0.0053702 0.0051045 0.0056988
10 AMR 0.0061843 0.0063284 0.0065907
10 EAS 0.0086799 0.0090581 0.0091298
10 EUR 0.0058815 0.0060049 0.0061312
10 SAS 0.0081091 0.0082448 0.0086279
11 AFR 0.0051038 0.0047643 0.0054421
11 AMR 0.0061504 0.0062567 0.0065811
11 EAS 0.0087048 0.0089563 0.0091293
11 EUR 0.0057273 0.0058646 0.0059475
11 SAS 0.0081458 0.0082203 0.0086106
12 AFR 0.0052336 0.0048435 0.0055285
12 AMR 0.0061647 0.0062722 0.0066160
12 EAS 0.0088507 0.0091833 0.0092980
12 EUR 0.0058835 0.0059865 0.0061495
12 SAS 0.0085005 0.0084572 0.0091331
13 AFR 0.0051338 0.0047588 0.0054669
13 AMR 0.0058467 0.0059489 0.0062847
13 EAS 0.0086166 0.0089850 0.0089645
13 EUR 0.0056813 0.0058049 0.0059074
13 SAS 0.0079485 0.0080400 0.0084311
14 AFR 0.0058491 0.0055279 0.0061819
14 AMR 0.0069236 0.0070836 0.0073920
14 EAS 0.0092338 0.0097126 0.0097585
14 EUR 0.0063719 0.0065804 0.0066770
14 SAS 0.0087328 0.0088611 0.0092879
15 AFR 0.0069205 0.0067038 0.0072805
15 AMR 0.0075491 0.0076851 0.0080371
15 EAS 0.0107938 0.0112109 0.0112988
15 EUR 0.0075873 0.0077744 0.0078511
15 SAS 0.0100833 0.0101590 0.0106255
16 AFR 0.0067101 0.0064605 0.0070518
16 AMR 0.0077841 0.0078624 0.0082867
16 EAS 0.0110409 0.0114166 0.0115555
16 EUR 0.0074827 0.0076739 0.0078211
16 SAS 0.0100990 0.0101592 0.0106840
17 AFR 0.0070385 0.0068052 0.0073412
17 AMR 0.0078579 0.0080042 0.0082180
17 EAS 0.0114246 0.0118422 0.0119096
17 EUR 0.0075552 0.0077852 0.0078145
17 SAS 0.0102826 0.0105113 0.0107783
18 AFR 0.0053748 0.0050216 0.0056865
18 AMR 0.0064686 0.0065122 0.0068916
18 EAS 0.0092433 0.0096255 0.0096967
18 EUR 0.0061722 0.0063152 0.0063982
18 SAS 0.0083972 0.0084671 0.0089623
19 AFR 0.0065154 0.0064078 0.0067781
19 AMR 0.0073732 0.0075864 0.0077798
19 EAS 0.0107155 0.0110315 0.0110440
19 EUR 0.0070417 0.0072541 0.0072739
19 SAS 0.0095512 0.0096150 0.0099775
20 AFR 0.0064594 0.0062060 0.0066644
20 AMR 0.0078739 0.0079705 0.0082688
20 EAS 0.0114298 0.0117419 0.0118613
20 EUR 0.0072520 0.0074422 0.0075192
20 SAS 0.0100663 0.0101533 0.0104775
21 AFR 0.0079544 0.0078804 0.0083141
21 AMR 0.0082498 0.0085883 0.0088090
21 EAS 0.0106827 0.0110631 0.0110567
21 EUR 0.0079347 0.0081427 0.0082329
21 SAS 0.0101535 0.0103601 0.0107176
22 AFR 0.0087059 0.0086329 0.0089909
22 AMR 0.0094276 0.0097295 0.0097832
22 EAS 0.0126112 0.0132342 0.0130122
22 EUR 0.0090470 0.0093067 0.0093290
22 SAS 0.0117030 0.0120662 0.0122487
23 AFR 0.0018961 0.0023549 0.0019652
23 AMR 0.0023216 0.0027562 0.0024143
23 EAS 0.0047907 0.0056040 0.0047650
23 EUR 0.0027532 0.0032940 0.0028181
23 SAS 0.0036354 0.0043134 0.0036627
df_total %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Error Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_total$chrom)), breaks = unique(df_total$chrom))

Version Author Date
9548985 theandyb 2025-07-14
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
cb6aa66 Andy Beck 2024-06-06
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
4255fdf Andy Beck 2024-05-21
df_total %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Error Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1")
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Version Author Date
9548985 theandyb 2025-07-14
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
cb6aa66 Andy Beck 2024-06-06
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
4255fdf Andy Beck 2024-05-21

Total Error Rates: without TH

df_total_noth %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  knitr::kable()
chrom Beagle Eagle SHAPEIT
1 0.0076521 0.0074991 0.0081145
2 0.0076647 0.0074667 0.0081643
3 0.0071878 0.0070196 0.0076684
4 0.0067061 0.0065728 0.0071506
5 0.0071902 0.0070086 0.0076810
6 0.0064784 0.0063175 0.0068826
7 0.0074391 0.0072982 0.0078961
8 0.0072741 0.0071112 0.0077785
9 0.0087028 0.0085344 0.0091643
10 0.0073034 0.0071957 0.0077402
11 0.0072545 0.0071127 0.0076998
12 0.0073676 0.0071869 0.0078629
13 0.0070782 0.0069520 0.0075517
14 0.0078292 0.0077546 0.0083515
15 0.0088513 0.0087992 0.0093716
16 0.0090042 0.0088870 0.0095468
17 0.0091358 0.0091251 0.0096319
18 0.0075749 0.0074640 0.0080646
19 0.0086534 0.0085857 0.0090404
20 0.0088541 0.0088080 0.0092697
21 0.0092530 0.0092396 0.0097647
22 0.0104660 0.0105487 0.0108801
23 0.0030794 0.0036645 0.0031251
df_total_noth %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable()
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
chrom SUPER Beagle Eagle SHAPEIT
1 AFR 0.0061541 0.0056486 0.0065314
1 AMR 0.0073666 0.0073292 0.0079129
1 EAS 0.0106916 0.0109163 0.0112412
1 EUR 0.0071962 0.0072442 0.0075011
1 SAS 0.0096538 0.0095749 0.0103064
2 AFR 0.0061388 0.0056225 0.0065608
2 AMR 0.0075898 0.0075022 0.0081132
2 EAS 0.0107179 0.0108905 0.0113975
2 EUR 0.0069836 0.0069560 0.0073585
2 SAS 0.0096647 0.0095134 0.0103140
3 AFR 0.0057432 0.0052412 0.0061616
3 AMR 0.0070168 0.0069471 0.0075380
3 EAS 0.0100329 0.0102511 0.0106030
3 EUR 0.0067507 0.0067821 0.0070954
3 SAS 0.0090197 0.0089031 0.0096771
4 AFR 0.0053117 0.0048314 0.0056544
4 AMR 0.0067435 0.0067364 0.0072623
4 EAS 0.0091007 0.0094034 0.0097654
4 EUR 0.0062322 0.0062823 0.0065560
4 SAS 0.0085118 0.0083951 0.0090426
5 AFR 0.0057888 0.0052588 0.0061717
5 AMR 0.0069223 0.0068988 0.0075261
5 EAS 0.0099982 0.0101669 0.0106601
5 EUR 0.0066684 0.0066730 0.0069973
5 SAS 0.0092144 0.0090709 0.0098365
6 AFR 0.0052882 0.0048326 0.0056455
6 AMR 0.0063160 0.0062851 0.0067728
6 EAS 0.0089145 0.0090832 0.0094091
6 EUR 0.0059026 0.0058674 0.0061651
6 SAS 0.0082162 0.0081050 0.0087478
7 AFR 0.0061038 0.0056994 0.0065178
7 AMR 0.0072283 0.0071565 0.0077147
7 EAS 0.0103415 0.0104331 0.0108755
7 EUR 0.0067620 0.0068192 0.0070783
7 SAS 0.0093305 0.0092548 0.0099534
8 AFR 0.0057580 0.0052287 0.0062152
8 AMR 0.0072094 0.0072296 0.0078531
8 EAS 0.0103658 0.0105017 0.0108167
8 EUR 0.0066998 0.0067455 0.0070381
8 SAS 0.0090675 0.0089602 0.0097137
9 AFR 0.0072790 0.0067742 0.0076794
9 AMR 0.0082460 0.0081980 0.0088147
9 EAS 0.0119425 0.0122030 0.0124844
9 EUR 0.0081866 0.0081938 0.0084512
9 SAS 0.0107116 0.0105605 0.0113243
10 AFR 0.0060101 0.0055700 0.0063808
10 AMR 0.0070975 0.0070947 0.0075821
10 EAS 0.0099579 0.0102006 0.0105497
10 EUR 0.0067013 0.0067321 0.0069622
10 SAS 0.0092032 0.0092410 0.0098090
11 AFR 0.0057508 0.0052706 0.0061522
11 AMR 0.0071722 0.0071385 0.0076623
11 EAS 0.0100594 0.0102104 0.0106357
11 EUR 0.0066157 0.0066985 0.0069070
11 SAS 0.0093714 0.0093244 0.0099305
12 AFR 0.0058881 0.0053664 0.0062714
12 AMR 0.0071270 0.0071253 0.0076752
12 EAS 0.0102030 0.0104132 0.0108250
12 EUR 0.0067653 0.0067907 0.0071100
12 SAS 0.0096107 0.0093571 0.0103676
13 AFR 0.0057598 0.0052336 0.0061534
13 AMR 0.0067713 0.0067205 0.0073271
13 EAS 0.0099220 0.0101621 0.0104243
13 EUR 0.0066041 0.0066269 0.0069020
13 SAS 0.0088785 0.0090787 0.0096048
14 AFR 0.0063748 0.0059296 0.0068014
14 AMR 0.0078321 0.0078557 0.0084076
14 EAS 0.0105339 0.0109551 0.0112067
14 EUR 0.0071596 0.0072943 0.0075659
14 SAS 0.0098157 0.0097760 0.0104966
15 AFR 0.0073277 0.0069690 0.0077226
15 AMR 0.0083891 0.0084119 0.0089976
15 EAS 0.0120937 0.0123599 0.0127375
15 EUR 0.0084371 0.0084965 0.0087513
15 SAS 0.0109737 0.0111161 0.0118033
16 AFR 0.0073035 0.0069346 0.0077028
16 AMR 0.0087787 0.0087222 0.0094068
16 EAS 0.0125706 0.0127711 0.0131870
16 EUR 0.0081882 0.0084785 0.0087961
16 SAS 0.0113959 0.0109937 0.0119946
17 AFR 0.0073358 0.0070736 0.0078345
17 AMR 0.0087838 0.0088201 0.0093046
17 EAS 0.0129842 0.0131864 0.0135194
17 EUR 0.0084777 0.0086132 0.0088212
17 SAS 0.0115283 0.0116718 0.0121370
18 AFR 0.0059493 0.0055207 0.0064076
18 AMR 0.0074577 0.0074038 0.0080159
18 EAS 0.0107453 0.0110003 0.0112748
18 EUR 0.0070523 0.0071887 0.0073948
18 SAS 0.0095802 0.0095075 0.0101851
19 AFR 0.0070700 0.0067483 0.0073763
19 AMR 0.0083913 0.0084724 0.0088096
19 EAS 0.0121217 0.0122739 0.0126333
19 EUR 0.0080380 0.0081286 0.0082796
19 SAS 0.0106572 0.0105645 0.0112617
20 AFR 0.0070020 0.0066413 0.0073049
20 AMR 0.0087767 0.0088334 0.0092888
20 EAS 0.0127205 0.0130084 0.0132947
20 EUR 0.0080504 0.0082237 0.0083524
20 SAS 0.0110950 0.0110681 0.0116302
21 AFR 0.0081714 0.0078706 0.0086193
21 AMR 0.0089086 0.0090239 0.0095120
21 EAS 0.0118682 0.0120773 0.0123458
21 EUR 0.0085628 0.0087016 0.0089665
21 SAS 0.0110190 0.0110979 0.0116987
22 AFR 0.0090094 0.0088317 0.0093308
22 AMR 0.0100386 0.0102130 0.0105044
22 EAS 0.0139285 0.0143327 0.0143294
22 EUR 0.0096566 0.0098559 0.0100114
22 SAS 0.0126854 0.0128169 0.0133210
23 AFR 0.0018961 0.0023549 0.0019652
23 AMR 0.0023216 0.0027562 0.0024143
23 EAS 0.0047907 0.0056040 0.0047650
23 EUR 0.0027532 0.0032940 0.0028181
23 SAS 0.0036354 0.0043134 0.0036627
df_total_noth %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Error Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_total_noth$chrom)), breaks = unique(df_total_noth$chrom))

Version Author Date
9548985 theandyb 2025-07-14
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
cb6aa66 Andy Beck 2024-06-06
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
4255fdf Andy Beck 2024-05-21
df_total_noth %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Error Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1") +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_total_noth$chrom)), breaks = unique(df_total_noth$chrom))
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Version Author Date
9548985 theandyb 2025-07-14
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
cb6aa66 Andy Beck 2024-06-06
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
4255fdf Andy Beck 2024-05-21

In X, do we see large variation among samples?

df_total %>%
  filter(chrom==23) %>%
  select(Beagle, Eagle, SHAPEIT) %>% summary()
     Beagle              Eagle              SHAPEIT         
 Min.   :0.0004964   Min.   :0.0008379   Min.   :0.0005717  
 1st Qu.:0.0018688   1st Qu.:0.0023121   1st Qu.:0.0019586  
 Median :0.0029121   Median :0.0034861   Median :0.0029834  
 Mean   :0.0030794   Mean   :0.0036645   Mean   :0.0031251  
 3rd Qu.:0.0041509   3rd Qu.:0.0048295   3rd Qu.:0.0041759  
 Max.   :0.0065490   Max.   :0.0074071   Max.   :0.0065881  

What range of values do we observe in the autosomes?

df_total_noth %>%
  select(Beagle, Eagle, SHAPEIT) %>%
  summarize(across(.cols = everything(),
                   .fns = list(
                     mean = ~mean(.x, na.rm =T),
                     sd = ~sd(.x, na.rm = T),
                     min = ~min(.x, na.rm=T),
                     max = ~max(.x, na.rm = T)
                   ),
                   .names = "{.col}_{.fn}") 
            ) %>%
  knitr::kable()
Beagle_mean Beagle_sd Beagle_min Beagle_max Eagle_mean Eagle_sd Eagle_min Eagle_max SHAPEIT_mean SHAPEIT_sd SHAPEIT_min SHAPEIT_max
0.0076089 0.0028562 0.0004964 0.0286303 0.0075472 0.0029323 0.0008379 0.0267024 0.0080498 0.002927 0.0005717 0.03858
df_total_noth %>%
  select(chrom, Beagle, Eagle, SHAPEIT) %>%
  group_by(chrom) %>%
  summarize(across(.cols = everything(),
                   .fns = list(
                     mean = ~mean(.x, na.rm =T),
                     sd = ~sd(.x, na.rm = T),
                     min = ~min(.x, na.rm=T),
                     max = ~max(.x, na.rm = T)
                   ),
                   .names = "{.col}_{.fn}") 
            ) %>%
  knitr::kable()
chrom Beagle_mean Beagle_sd Beagle_min Beagle_max Eagle_mean Eagle_sd Eagle_min Eagle_max SHAPEIT_mean SHAPEIT_sd SHAPEIT_min SHAPEIT_max
1 0.0076521 0.0023322 0.0023801 0.0136999 0.0074991 0.0025325 0.0030514 0.0139830 0.0081145 0.0023436 0.0027549 0.0144356
2 0.0076647 0.0023303 0.0029286 0.0133430 0.0074667 0.0025172 0.0023141 0.0139171 0.0081643 0.0023535 0.0040192 0.0141955
3 0.0071878 0.0022068 0.0018160 0.0127320 0.0070196 0.0023905 0.0022519 0.0128360 0.0076684 0.0022175 0.0026375 0.0137675
4 0.0067061 0.0020228 0.0023847 0.0117561 0.0065728 0.0022239 0.0020223 0.0122799 0.0071506 0.0020349 0.0026897 0.0118537
5 0.0071902 0.0022701 0.0027259 0.0126031 0.0070086 0.0024388 0.0019837 0.0127815 0.0076810 0.0023090 0.0033045 0.0130985
6 0.0064784 0.0019903 0.0019080 0.0132438 0.0063175 0.0021561 0.0017240 0.0132704 0.0068826 0.0019991 0.0023244 0.0135365
7 0.0074391 0.0022364 0.0029074 0.0150164 0.0072982 0.0023531 0.0028348 0.0135418 0.0078961 0.0022286 0.0030710 0.0146751
8 0.0072741 0.0023261 0.0028526 0.0135109 0.0071112 0.0025080 0.0026864 0.0137193 0.0077785 0.0023149 0.0035202 0.0149419
9 0.0087028 0.0024156 0.0037646 0.0145061 0.0085344 0.0026200 0.0038298 0.0152881 0.0091643 0.0024335 0.0041561 0.0151824
10 0.0073034 0.0021106 0.0023978 0.0123300 0.0071957 0.0022981 0.0022696 0.0126610 0.0077402 0.0021356 0.0033953 0.0129421
11 0.0072545 0.0023517 0.0024552 0.0132898 0.0071127 0.0025089 0.0021710 0.0137564 0.0076998 0.0023498 0.0029189 0.0138887
12 0.0073676 0.0024640 0.0031297 0.0286303 0.0071869 0.0025879 0.0026982 0.0267024 0.0078629 0.0026569 0.0032827 0.0385800
13 0.0070782 0.0022524 0.0022073 0.0127083 0.0069520 0.0024339 0.0020488 0.0133164 0.0075517 0.0022353 0.0034269 0.0134057
14 0.0078292 0.0023410 0.0023962 0.0159714 0.0077546 0.0025490 0.0022465 0.0166544 0.0083515 0.0024001 0.0031900 0.0157087
15 0.0088513 0.0026191 0.0025277 0.0165449 0.0087992 0.0027724 0.0028078 0.0174337 0.0093716 0.0026636 0.0032533 0.0174043
16 0.0090042 0.0028986 0.0025181 0.0173381 0.0088870 0.0029658 0.0026695 0.0169698 0.0095468 0.0029068 0.0035420 0.0177347
17 0.0091358 0.0029524 0.0030712 0.0173353 0.0091251 0.0030734 0.0028818 0.0176482 0.0096319 0.0029560 0.0035134 0.0174917
18 0.0075749 0.0024421 0.0019858 0.0141914 0.0074640 0.0025959 0.0021564 0.0147436 0.0080646 0.0024261 0.0028701 0.0144952
19 0.0086534 0.0026488 0.0010857 0.0154416 0.0085857 0.0027182 0.0021404 0.0154304 0.0090404 0.0027148 0.0011167 0.0169087
20 0.0088541 0.0029581 0.0029367 0.0205275 0.0088080 0.0031023 0.0029535 0.0219209 0.0092697 0.0029872 0.0033721 0.0209013
21 0.0092530 0.0024265 0.0032546 0.0181752 0.0092396 0.0025532 0.0037141 0.0161322 0.0097647 0.0024139 0.0041352 0.0164855
22 0.0104660 0.0029920 0.0026342 0.0211825 0.0105487 0.0031360 0.0037631 0.0219650 0.0108801 0.0030757 0.0034809 0.0223834
23 0.0030794 0.0013598 0.0004964 0.0065490 0.0036645 0.0014956 0.0008379 0.0074071 0.0031251 0.0013461 0.0005717 0.0065881

Let’s first do a hypothesis test to compare the mean error rates in X versus the autosomes.

# Beagle
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(Beagle)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00487   0.00795   0.00308      100.       0     1638.  0.00478   0.00497
# ℹ 2 more variables: method <chr>, alternative <chr>
# Eagle
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00418   0.00784   0.00366      78.5       0     1591.  0.00407   0.00428
# ℹ 2 more variables: method <chr>, alternative <chr>
# SHAPEIT
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00530   0.00842   0.00313      109.       0     1667.  0.00520   0.00539
# ℹ 2 more variables: method <chr>, alternative <chr>

Additionally, I would like to test the null hypothesis that the error rates are the same across chromosomes for each method:

mod_fit <- df_total_noth %>%
  filter(chrom < 23) %>%
  {lmerTest::lmer(Beagle ~ chrom + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(method = "Beagle")
Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF
mod_fit <- df_total_noth %>%
  filter(chrom < 23) %>%
  {lmerTest::lmer(Eagle ~ chrom + (1|pair_id), data = .)}

df_anova <- bind_rows(df_anova, {anova(mod_fit) %>% broom::tidy() %>% mutate(method = "Eagle")})
Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF
mod_fit <- df_total_noth %>%
  filter(chrom < 23) %>%
  {lmerTest::lmer(SHAPEIT ~ chrom + (1|pair_id), data = .)}

df_anova <- bind_rows(df_anova, {anova(mod_fit) %>% broom::tidy() %>% mutate(method = "SHAPEIT")})
Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF
df_anova %>%
  knitr::kable()
term sumsq meansq NumDF DenDF statistic p.value method
chrom 0.0068825 0.0068825 1 12641 4603.281 0 Beagle
chrom 0.0079801 0.0079801 1 12641 5635.171 0 Eagle
chrom 0.0068546 0.0068546 1 12641 4397.972 0 SHAPEIT

For each chromosome, we will test several hypotheses:

  1. Are the error rates for Beagle, Eagle, and SHAPEIT the same?
  2. If the above does not hold, when we do pairwise comparisons between the methods, are error rates the same?
  3. Do error rates differ by population? If so, do above tests separately for each population.

For the first test, I’ll use a linear mixed model with random intercepts for each individual/synthetic diploid. This will also allow me to do contrasts for the pairwise comparisons.

mod_fit <- df_total_noth %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)

for(i in 2:23){
  mod_fit <- df_total_noth %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
  
  df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pairwise <- df_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}

df_anova %>% knitr::kable()
term sumsq meansq NumDF DenDF statistic p.value chrom
method 0.0001236 0.0000618 2 1202 656.00360 0 1
method 0.0001556 0.0000778 2 1202 823.78246 0 2
method 0.0001365 0.0000682 2 1202 733.34212 0 3
method 0.0001102 0.0000551 2 1202 559.83128 0 4
method 0.0001456 0.0000728 2 1202 731.43837 0 5
method 0.0001020 0.0000510 2 1202 629.02561 0 6
method 0.0001176 0.0000588 2 1202 576.07381 0 7
method 0.0001457 0.0000729 2 1202 494.42277 0 8
method 0.0001280 0.0000640 2 1202 496.03954 0 9
method 0.0001001 0.0000500 2 1202 462.22172 0 10
method 0.0001130 0.0000565 2 1202 463.45512 0 11
method 0.0001475 0.0000737 2 1202 406.63922 0 12
method 0.0001203 0.0000602 2 1202 340.63110 0 13
method 0.0001273 0.0000637 2 1202 405.14772 0 14
method 0.0001206 0.0000603 2 1202 368.10822 0 15
method 0.0001492 0.0000746 2 1202 299.00932 0 16
method 0.0001009 0.0000505 2 1202 245.86294 0 17
method 0.0001230 0.0000615 2 1202 414.98049 0 18
method 0.0000725 0.0000362 2 1202 181.45836 0 19
method 0.0000779 0.0000389 2 1202 207.08658 0 20
method 0.0001079 0.0000540 2 1202 220.66307 0 21
method 0.0000578 0.0000289 2 1202 96.57538 0 22
method 0.0002118 0.0001059 2 1998 2542.00116 0 23
df_pairwise %>% knitr::kable()
term contrast null.value estimate std.error df statistic adj.p.value chrom
method Beagle - Eagle 0 0.0001530 1.77e-05 1202 8.6488600 0.0000000 1
method Beagle - SHAPEIT 0 -0.0004624 1.77e-05 1202 -26.1370756 0.0000000 1
method Eagle - SHAPEIT 0 -0.0006154 1.77e-05 1202 -34.7859356 0.0000000 1
method Beagle - Eagle 0 0.0001980 1.77e-05 1202 11.1769601 0.0000000 2
method Beagle - SHAPEIT 0 -0.0004996 1.77e-05 1202 -28.2047198 0.0000000 2
method Eagle - SHAPEIT 0 -0.0006976 1.77e-05 1202 -39.3816799 0.0000000 2
method Beagle - Eagle 0 0.0001682 1.76e-05 1202 9.5679959 0.0000000 3
method Beagle - SHAPEIT 0 -0.0004806 1.76e-05 1202 -27.3306914 0.0000000 3
method Eagle - SHAPEIT 0 -0.0006488 1.76e-05 1202 -36.8986873 0.0000000 3
method Beagle - Eagle 0 0.0001333 1.81e-05 1202 7.3721385 0.0000000 4
method Beagle - SHAPEIT 0 -0.0004445 1.81e-05 1202 -24.5802640 0.0000000 4
method Eagle - SHAPEIT 0 -0.0005778 1.81e-05 1202 -31.9524025 0.0000000 4
method Beagle - Eagle 0 0.0001816 1.82e-05 1202 9.9851073 0.0000000 5
method Beagle - SHAPEIT 0 -0.0004907 1.82e-05 1202 -26.9821360 0.0000000 5
method Eagle - SHAPEIT 0 -0.0006723 1.82e-05 1202 -36.9672433 0.0000000 5
method Beagle - Eagle 0 0.0001609 1.64e-05 1202 9.8033434 0.0000000 6
method Beagle - SHAPEIT 0 -0.0004041 1.64e-05 1202 -24.6188170 0.0000000 6
method Eagle - SHAPEIT 0 -0.0005651 1.64e-05 1202 -34.4221605 0.0000000 6
method Beagle - Eagle 0 0.0001409 1.84e-05 1202 7.6532132 0.0000000 7
method Beagle - SHAPEIT 0 -0.0004569 1.84e-05 1202 -24.8122126 0.0000000 7
method Eagle - SHAPEIT 0 -0.0005979 1.84e-05 1202 -32.4654258 0.0000000 7
method Beagle - Eagle 0 0.0001629 2.21e-05 1202 7.3614752 0.0000000 8
method Beagle - SHAPEIT 0 -0.0005044 2.21e-05 1202 -22.7954906 0.0000000 8
method Eagle - SHAPEIT 0 -0.0006673 2.21e-05 1202 -30.1569658 0.0000000 8
method Beagle - Eagle 0 0.0001684 2.07e-05 1202 8.1314831 0.0000000 9
method Beagle - SHAPEIT 0 -0.0004615 2.07e-05 1202 -22.2870296 0.0000000 9
method Eagle - SHAPEIT 0 -0.0006299 2.07e-05 1202 -30.4185127 0.0000000 9
method Beagle - Eagle 0 0.0001077 1.90e-05 1202 5.6775925 0.0000001 10
method Beagle - SHAPEIT 0 -0.0004368 1.90e-05 1202 -23.0292590 0.0000000 10
method Eagle - SHAPEIT 0 -0.0005445 1.90e-05 1202 -28.7068515 0.0000000 10
method Beagle - Eagle 0 0.0001419 2.01e-05 1202 7.0497074 0.0000000 11
method Beagle - SHAPEIT 0 -0.0004452 2.01e-05 1202 -22.1248811 0.0000000 11
method Eagle - SHAPEIT 0 -0.0005871 2.01e-05 1202 -29.1745885 0.0000000 11
method Beagle - Eagle 0 0.0001807 2.45e-05 1202 7.3622141 0.0000000 12
method Beagle - SHAPEIT 0 -0.0004953 2.45e-05 1202 -20.1790520 0.0000000 12
method Eagle - SHAPEIT 0 -0.0006760 2.45e-05 1202 -27.5412661 0.0000000 12
method Beagle - Eagle 0 0.0001262 2.42e-05 1202 5.2086356 0.0000007 13
method Beagle - SHAPEIT 0 -0.0004735 2.42e-05 1202 -19.5451570 0.0000000 13
method Eagle - SHAPEIT 0 -0.0005997 2.42e-05 1202 -24.7537925 0.0000000 13
method Beagle - Eagle 0 0.0000746 2.28e-05 1202 3.2639710 0.0032378 14
method Beagle - SHAPEIT 0 -0.0005222 2.28e-05 1202 -22.8574295 0.0000000 14
method Eagle - SHAPEIT 0 -0.0005968 2.28e-05 1202 -26.1214005 0.0000000 14
method Beagle - Eagle 0 0.0000521 2.33e-05 1202 2.2312906 0.0664182 15
method Beagle - SHAPEIT 0 -0.0005203 2.33e-05 1202 -22.3029015 0.0000000 15
method Eagle - SHAPEIT 0 -0.0005724 2.33e-05 1202 -24.5341921 0.0000000 15
method Beagle - Eagle 0 0.0001172 2.88e-05 1202 4.0717243 0.0001470 16
method Beagle - SHAPEIT 0 -0.0005426 2.88e-05 1202 -18.8466611 0.0000000 16
method Eagle - SHAPEIT 0 -0.0006598 2.88e-05 1202 -22.9183854 0.0000000 16
method Beagle - Eagle 0 0.0000108 2.61e-05 1202 0.4119101 0.9107351 17
method Beagle - SHAPEIT 0 -0.0004960 2.61e-05 1202 -18.9947521 0.0000000 17
method Eagle - SHAPEIT 0 -0.0005068 2.61e-05 1202 -19.4066622 0.0000000 17
method Beagle - Eagle 0 0.0001109 2.22e-05 1202 4.9985018 0.0000020 18
method Beagle - SHAPEIT 0 -0.0004897 2.22e-05 1202 -22.0717069 0.0000000 18
method Eagle - SHAPEIT 0 -0.0006006 2.22e-05 1202 -27.0702087 0.0000000 18
method Beagle - Eagle 0 0.0000677 2.58e-05 1202 2.6289886 0.0235566 19
method Beagle - SHAPEIT 0 -0.0003870 2.58e-05 1202 -15.0257580 0.0000000 19
method Eagle - SHAPEIT 0 -0.0004547 2.58e-05 1202 -17.6547467 0.0000000 19
method Beagle - Eagle 0 0.0000461 2.50e-05 1202 1.8443352 0.1557312 20
method Beagle - SHAPEIT 0 -0.0004156 2.50e-05 1202 -16.6300028 0.0000000 20
method Eagle - SHAPEIT 0 -0.0004617 2.50e-05 1202 -18.4743380 0.0000000 20
method Beagle - Eagle 0 0.0000134 2.85e-05 1202 0.4700150 0.8853898 21
method Beagle - SHAPEIT 0 -0.0005117 2.85e-05 1202 -17.9536956 0.0000000 21
method Eagle - SHAPEIT 0 -0.0005251 2.85e-05 1202 -18.4237107 0.0000000 21
method Beagle - Eagle 0 -0.0000827 3.15e-05 1202 -2.6225872 0.0239835 22
method Beagle - SHAPEIT 0 -0.0004141 3.15e-05 1202 -13.1309636 0.0000000 22
method Eagle - SHAPEIT 0 -0.0003314 3.15e-05 1202 -10.5083765 0.0000000 22
method Beagle - Eagle 0 -0.0005851 9.10e-06 1998 -64.0995718 0.0000000 23
method Beagle - SHAPEIT 0 -0.0000457 9.10e-06 1998 -5.0047233 0.0000018 23
method Eagle - SHAPEIT 0 0.0005394 9.10e-06 1998 59.0948484 0.0000000 23
df_pairwise %>%
  filter(adj.p.value > 0.05) %>%
  knitr::kable()
term contrast null.value estimate std.error df statistic adj.p.value chrom
method Beagle - Eagle 0 5.21e-05 2.33e-05 1202 2.2312906 0.0664182 15
method Beagle - Eagle 0 1.08e-05 2.61e-05 1202 0.4119101 0.9107351 17
method Beagle - Eagle 0 4.61e-05 2.50e-05 1202 1.8443352 0.1557312 20
method Beagle - Eagle 0 1.34e-05 2.85e-05 1202 0.4700150 0.8853898 21

Now let’s do these comparisons within each super-population:

mod_fit <- df_total_noth %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}

df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)

for(i in 2:23){
  mod_fit <- df_total_noth %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
  
  df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
  df_pop_pop <- df_pop_pop %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}

df_pop_anova %>% knitr::kable()
term sumsq meansq NumDF DenDF statistic p.value chrom
method 0.0000970 0.0000485 2 1194.0000 684.993557 0 1
SUPER 0.0000403 0.0000101 4 597.0000 142.135219 0 1
method:SUPER 0.0000287 0.0000036 8 1194.0000 50.640353 0 1
method 0.0001270 0.0000635 2 1194.0000 834.414662 0 2
SUPER 0.0000456 0.0000114 4 597.0000 149.664197 0 2
method:SUPER 0.0000226 0.0000028 8 1194.0000 37.178475 0 2
method 0.0001072 0.0000536 2 1194.0000 751.821151 0 3
SUPER 0.0000396 0.0000099 4 597.0000 138.951458 0 3
method:SUPER 0.0000267 0.0000033 8 1194.0000 46.847777 0 3
method 0.0000892 0.0000446 2 1194.0000 577.945676 0 4
SUPER 0.0000448 0.0000112 4 597.0000 145.126286 0 4
method:SUPER 0.0000261 0.0000033 8 1194.0000 42.270907 0 4
method 0.0001184 0.0000592 2 1194.0000 756.839178 0 5
SUPER 0.0000413 0.0000103 4 597.0000 131.905501 0 5
method:SUPER 0.0000263 0.0000033 8 1194.0000 42.028809 0 5
method 0.0000792 0.0000396 2 1194.0000 609.514893 0 6
SUPER 0.0000322 0.0000081 4 597.0000 124.060370 0 6
method:SUPER 0.0000200 0.0000025 8 1194.0000 38.422997 0 6
method 0.0000952 0.0000476 2 1194.0000 541.823084 0 7
SUPER 0.0000468 0.0000117 4 596.9999 133.235429 0 7
method:SUPER 0.0000178 0.0000022 8 1194.0000 25.282506 0 7
method 0.0001089 0.0000545 2 1194.0000 448.195973 0 8
SUPER 0.0000662 0.0000166 4 597.0000 136.218054 0 8
method:SUPER 0.0000321 0.0000040 8 1194.0000 32.986322 0 8
method 0.0000978 0.0000489 2 1194.0000 467.435725 0 9
SUPER 0.0000558 0.0000139 4 597.0000 133.284760 0 9
method:SUPER 0.0000302 0.0000038 8 1194.0000 36.062684 0 9
method 0.0000800 0.0000400 2 1194.0000 451.764809 0 10
SUPER 0.0000498 0.0000124 4 596.9999 140.515094 0 10
method:SUPER 0.0000244 0.0000030 8 1194.0000 34.400393 0 10
method 0.0000880 0.0000440 2 1194.0000 435.589782 0 11
SUPER 0.0000532 0.0000133 4 596.9999 131.798942 0 11
method:SUPER 0.0000259 0.0000032 8 1194.0000 32.068560 0 11
method 0.0001238 0.0000619 2 1194.0001 398.164349 0 12
SUPER 0.0000701 0.0000175 4 596.9996 112.723771 0 12
method:SUPER 0.0000323 0.0000040 8 1194.0001 25.975115 0 12
method 0.0000906 0.0000453 2 1194.0000 305.359265 0 13
SUPER 0.0000761 0.0000190 4 597.0000 128.286830 0 13
method:SUPER 0.0000352 0.0000044 8 1194.0000 29.645340 0 13
method 0.0001040 0.0000520 2 1194.0000 395.555364 0 14
SUPER 0.0000617 0.0000154 4 597.0000 117.352113 0 14
method:SUPER 0.0000318 0.0000040 8 1194.0000 30.269096 0 14
method 0.0001049 0.0000524 2 1194.0000 361.313934 0 15
SUPER 0.0000679 0.0000170 4 597.0000 116.984755 0 15
method:SUPER 0.0000236 0.0000029 8 1194.0000 20.318197 0 15
method 0.0001297 0.0000649 2 1194.0000 283.660734 0 16
SUPER 0.0001029 0.0000257 4 596.9999 112.494890 0 16
method:SUPER 0.0000269 0.0000034 8 1194.0000 14.684099 0 16
method 0.0000805 0.0000403 2 1194.0000 208.716218 0 17
SUPER 0.0000959 0.0000240 4 597.0000 124.243178 0 17
method:SUPER 0.0000164 0.0000021 8 1194.0000 10.644324 0 17
method 0.0000938 0.0000469 2 1194.0000 372.147639 0 18
SUPER 0.0000713 0.0000178 4 597.0000 141.355742 0 18
method:SUPER 0.0000276 0.0000034 8 1194.0000 27.352646 0 18
method 0.0000639 0.0000320 2 1194.0000 172.053799 0 19
SUPER 0.0000894 0.0000223 4 597.0000 120.274053 0 19
method:SUPER 0.0000182 0.0000023 8 1194.0000 12.225247 0 19
method 0.0000661 0.0000330 2 1194.0000 193.320266 0 20
SUPER 0.0000866 0.0000217 4 597.0000 126.782913 0 20
method:SUPER 0.0000220 0.0000027 8 1194.0000 16.080003 0 20
method 0.0000882 0.0000441 2 1194.0000 190.791026 0 21
SUPER 0.0000665 0.0000166 4 597.0000 71.906930 0 21
method:SUPER 0.0000180 0.0000023 8 1194.0000 9.744354 0 21
method 0.0000520 0.0000260 2 1194.0000 90.499127 0 22
SUPER 0.0000934 0.0000234 4 597.0000 81.308769 0 22
method:SUPER 0.0000168 0.0000021 8 1194.0000 7.295923 0 22
method 0.0002118 0.0001059 2 1990.0000 3255.331545 0 23
SUPER 0.0000458 0.0000114 4 994.9999 351.584878 0 23
method:SUPER 0.0000185 0.0000023 8 1990.0000 71.084254 0 23
df_pop_pairwise %>% knitr::kable()
SUPER term contrast null.value estimate std.error df statistic adj.p.value chrom
AFR method Beagle - Eagle 0 0.0005055 2.65e-05 1194 19.0440527 0.0000000 1
AFR method Beagle - SHAPEIT 0 -0.0003773 2.65e-05 1194 -14.2151091 0.0000000 1
AFR method Eagle - SHAPEIT 0 -0.0008828 2.65e-05 1194 -33.2591618 0.0000000 1
AMR method Beagle - Eagle 0 0.0000373 3.22e-05 1194 1.1614326 0.4765626 1
AMR method Beagle - SHAPEIT 0 -0.0005463 3.22e-05 1194 -16.9923411 0.0000000 1
AMR method Eagle - SHAPEIT 0 -0.0005837 3.22e-05 1194 -18.1537736 0.0000000 1
EAS method Beagle - Eagle 0 -0.0002248 4.44e-05 1194 -5.0678399 0.0000014 1
EAS method Beagle - SHAPEIT 0 -0.0005496 4.44e-05 1194 -12.3933265 0.0000000 1
EAS method Eagle - SHAPEIT 0 -0.0003249 4.44e-05 1194 -7.3254866 0.0000000 1
EUR method Beagle - Eagle 0 -0.0000480 3.64e-05 1194 -1.3200650 0.3842343 1
EUR method Beagle - SHAPEIT 0 -0.0003049 3.64e-05 1194 -8.3808704 0.0000000 1
EUR method Eagle - SHAPEIT 0 -0.0002569 3.64e-05 1194 -7.0608053 0.0000000 1
SAS method Beagle - Eagle 0 0.0000789 4.08e-05 1194 1.9338974 0.1296453 1
SAS method Beagle - SHAPEIT 0 -0.0006526 4.08e-05 1194 -15.9880567 0.0000000 1
SAS method Eagle - SHAPEIT 0 -0.0007315 4.08e-05 1194 -17.9219541 0.0000000 1
AFR method Beagle - Eagle 0 0.0005163 2.75e-05 1194 18.7620053 0.0000000 2
AFR method Beagle - SHAPEIT 0 -0.0004220 2.75e-05 1194 -15.3352301 0.0000000 2
AFR method Eagle - SHAPEIT 0 -0.0009383 2.75e-05 1194 -34.0972354 0.0000000 2
AMR method Beagle - Eagle 0 0.0000877 3.33e-05 1194 2.6305211 0.0234572 2
AMR method Beagle - SHAPEIT 0 -0.0005233 3.33e-05 1194 -15.7005189 0.0000000 2
AMR method Eagle - SHAPEIT 0 -0.0006110 3.33e-05 1194 -18.3310400 0.0000000 2
EAS method Beagle - Eagle 0 -0.0001726 4.60e-05 1194 -3.7529039 0.0005369 2
EAS method Beagle - SHAPEIT 0 -0.0006795 4.60e-05 1194 -14.7788721 0.0000000 2
EAS method Eagle - SHAPEIT 0 -0.0005070 4.60e-05 1194 -11.0259682 0.0000000 2
EUR method Beagle - Eagle 0 0.0000276 3.77e-05 1194 0.7308715 0.7452005 2
EUR method Beagle - SHAPEIT 0 -0.0003749 3.77e-05 1194 -9.9396659 0.0000000 2
EUR method Eagle - SHAPEIT 0 -0.0004025 3.77e-05 1194 -10.6705374 0.0000000 2
SAS method Beagle - Eagle 0 0.0001513 4.23e-05 1194 3.5759958 0.0010564 2
SAS method Beagle - SHAPEIT 0 -0.0006492 4.23e-05 1194 -15.3418032 0.0000000 2
SAS method Eagle - SHAPEIT 0 -0.0008006 4.23e-05 1194 -18.9177990 0.0000000 2
AFR method Beagle - Eagle 0 0.0005019 2.66e-05 1194 18.8439898 0.0000000 3
AFR method Beagle - SHAPEIT 0 -0.0004184 2.66e-05 1194 -15.7075197 0.0000000 3
AFR method Eagle - SHAPEIT 0 -0.0009203 2.66e-05 1194 -34.5515095 0.0000000 3
AMR method Beagle - Eagle 0 0.0000697 3.23e-05 1194 2.1604475 0.0785432 3
AMR method Beagle - SHAPEIT 0 -0.0005212 3.23e-05 1194 -16.1544877 0.0000000 3
AMR method Eagle - SHAPEIT 0 -0.0005909 3.23e-05 1194 -18.3149352 0.0000000 3
EAS method Beagle - Eagle 0 -0.0002182 4.45e-05 1194 -4.9020919 0.0000032 3
EAS method Beagle - SHAPEIT 0 -0.0005701 4.45e-05 1194 -12.8090854 0.0000000 3
EAS method Eagle - SHAPEIT 0 -0.0003519 4.45e-05 1194 -7.9069935 0.0000000 3
EUR method Beagle - Eagle 0 -0.0000314 3.65e-05 1194 -0.8600196 0.6656372 3
EUR method Beagle - SHAPEIT 0 -0.0003447 3.65e-05 1194 -9.4407418 0.0000000 3
EUR method Eagle - SHAPEIT 0 -0.0003133 3.65e-05 1194 -8.5807222 0.0000000 3
SAS method Beagle - Eagle 0 0.0001166 4.10e-05 1194 2.8459360 0.0125104 3
SAS method Beagle - SHAPEIT 0 -0.0006574 4.10e-05 1194 -16.0492012 0.0000000 3
SAS method Eagle - SHAPEIT 0 -0.0007740 4.10e-05 1194 -18.8951372 0.0000000 3
AFR method Beagle - Eagle 0 0.0004803 2.77e-05 1194 17.3264765 0.0000000 4
AFR method Beagle - SHAPEIT 0 -0.0003427 2.77e-05 1194 -12.3642277 0.0000000 4
AFR method Eagle - SHAPEIT 0 -0.0008230 2.77e-05 1194 -29.6907042 0.0000000 4
AMR method Beagle - Eagle 0 0.0000071 3.36e-05 1194 0.2106180 0.9758425 4
AMR method Beagle - SHAPEIT 0 -0.0005188 3.36e-05 1194 -15.4513339 0.0000000 4
AMR method Eagle - SHAPEIT 0 -0.0005258 3.36e-05 1194 -15.6619519 0.0000000 4
EAS method Beagle - Eagle 0 -0.0003027 4.63e-05 1194 -6.5366803 0.0000000 4
EAS method Beagle - SHAPEIT 0 -0.0006647 4.63e-05 1194 -14.3531006 0.0000000 4
EAS method Eagle - SHAPEIT 0 -0.0003620 4.63e-05 1194 -7.8164202 0.0000000 4
EUR method Beagle - Eagle 0 -0.0000502 3.80e-05 1194 -1.3208221 0.3838147 4
EUR method Beagle - SHAPEIT 0 -0.0003238 3.80e-05 1194 -8.5229063 0.0000000 4
EUR method Eagle - SHAPEIT 0 -0.0002736 3.80e-05 1194 -7.2020843 0.0000000 4
SAS method Beagle - Eagle 0 0.0001167 4.26e-05 1194 2.7371383 0.0172855 4
SAS method Beagle - SHAPEIT 0 -0.0005308 4.26e-05 1194 -12.4524035 0.0000000 4
SAS method Eagle - SHAPEIT 0 -0.0006474 4.26e-05 1194 -15.1895418 0.0000000 4
AFR method Beagle - Eagle 0 0.0005300 2.79e-05 1194 19.0005097 0.0000000 5
AFR method Beagle - SHAPEIT 0 -0.0003829 2.79e-05 1194 -13.7265817 0.0000000 5
AFR method Eagle - SHAPEIT 0 -0.0009129 2.79e-05 1194 -32.7270914 0.0000000 5
AMR method Beagle - Eagle 0 0.0000235 3.38e-05 1194 0.6966320 0.7655009 5
AMR method Beagle - SHAPEIT 0 -0.0006038 3.38e-05 1194 -17.8693578 0.0000000 5
AMR method Eagle - SHAPEIT 0 -0.0006273 3.38e-05 1194 -18.5659898 0.0000000 5
EAS method Beagle - Eagle 0 -0.0001687 4.66e-05 1194 -3.6196228 0.0008965 5
EAS method Beagle - SHAPEIT 0 -0.0006619 4.66e-05 1194 -14.2010224 0.0000000 5
EAS method Eagle - SHAPEIT 0 -0.0004932 4.66e-05 1194 -10.5813996 0.0000000 5
EUR method Beagle - Eagle 0 -0.0000046 3.82e-05 1194 -0.1198941 0.9921065 5
EUR method Beagle - SHAPEIT 0 -0.0003289 3.82e-05 1194 -8.6024373 0.0000000 5
EUR method Eagle - SHAPEIT 0 -0.0003243 3.82e-05 1194 -8.4825432 0.0000000 5
SAS method Beagle - Eagle 0 0.0001435 4.29e-05 1194 3.3457221 0.0024368 5
SAS method Beagle - SHAPEIT 0 -0.0006222 4.29e-05 1194 -14.5038132 0.0000000 5
SAS method Eagle - SHAPEIT 0 -0.0007657 4.29e-05 1194 -17.8495353 0.0000000 5
AFR method Beagle - Eagle 0 0.0004556 2.54e-05 1194 17.9232098 0.0000000 6
AFR method Beagle - SHAPEIT 0 -0.0003573 2.54e-05 1194 -14.0579172 0.0000000 6
AFR method Eagle - SHAPEIT 0 -0.0008129 2.54e-05 1194 -31.9811270 0.0000000 6
AMR method Beagle - Eagle 0 0.0000309 3.08e-05 1194 1.0047598 0.5739814 6
AMR method Beagle - SHAPEIT 0 -0.0004568 3.08e-05 1194 -14.8351085 0.0000000 6
AMR method Eagle - SHAPEIT 0 -0.0004877 3.08e-05 1194 -15.8398683 0.0000000 6
EAS method Beagle - Eagle 0 -0.0001687 4.25e-05 1194 -3.9722441 0.0002226 6
EAS method Beagle - SHAPEIT 0 -0.0004946 4.25e-05 1194 -11.6451918 0.0000000 6
EAS method Eagle - SHAPEIT 0 -0.0003259 4.25e-05 1194 -7.6729477 0.0000000 6
EUR method Beagle - Eagle 0 0.0000351 3.48e-05 1194 1.0086359 0.5715297 6
EUR method Beagle - SHAPEIT 0 -0.0002625 3.48e-05 1194 -7.5354147 0.0000000 6
EUR method Eagle - SHAPEIT 0 -0.0002977 3.48e-05 1194 -8.5440506 0.0000000 6
SAS method Beagle - Eagle 0 0.0001112 3.91e-05 1194 2.8449610 0.0125474 6
SAS method Beagle - SHAPEIT 0 -0.0005316 3.91e-05 1194 -13.5994183 0.0000000 6
SAS method Eagle - SHAPEIT 0 -0.0006428 3.91e-05 1194 -16.4443792 0.0000000 6
AFR method Beagle - Eagle 0 0.0004044 2.96e-05 1194 13.6777630 0.0000000 7
AFR method Beagle - SHAPEIT 0 -0.0004139 2.96e-05 1194 -13.9984462 0.0000000 7
AFR method Eagle - SHAPEIT 0 -0.0008184 2.96e-05 1194 -27.6762091 0.0000000 7
AMR method Beagle - Eagle 0 0.0000718 3.58e-05 1194 2.0038332 0.1116978 7
AMR method Beagle - SHAPEIT 0 -0.0004864 3.58e-05 1194 -13.5804758 0.0000000 7
AMR method Eagle - SHAPEIT 0 -0.0005582 3.58e-05 1194 -15.5843090 0.0000000 7
EAS method Beagle - Eagle 0 -0.0000917 4.94e-05 1194 -1.8552389 0.1523649 7
EAS method Beagle - SHAPEIT 0 -0.0005340 4.94e-05 1194 -10.8082895 0.0000000 7
EAS method Eagle - SHAPEIT 0 -0.0004423 4.94e-05 1194 -8.9530505 0.0000000 7
EUR method Beagle - Eagle 0 -0.0000572 4.05e-05 1194 -1.4112475 0.3353662 7
EUR method Beagle - SHAPEIT 0 -0.0003163 4.05e-05 1194 -7.8036290 0.0000000 7
EUR method Eagle - SHAPEIT 0 -0.0002591 4.05e-05 1194 -6.3923814 0.0000000 7
SAS method Beagle - Eagle 0 0.0000757 4.55e-05 1194 1.6652420 0.2190879 7
SAS method Beagle - SHAPEIT 0 -0.0006228 4.55e-05 1194 -13.6977318 0.0000000 7
SAS method Eagle - SHAPEIT 0 -0.0006986 4.55e-05 1194 -15.3629738 0.0000000 7
AFR method Beagle - Eagle 0 0.0005292 3.48e-05 1194 15.2191879 0.0000000 8
AFR method Beagle - SHAPEIT 0 -0.0004572 3.48e-05 1194 -13.1492904 0.0000000 8
AFR method Eagle - SHAPEIT 0 -0.0009865 3.48e-05 1194 -28.3684784 0.0000000 8
AMR method Beagle - Eagle 0 -0.0000202 4.21e-05 1194 -0.4797532 0.8808918 8
AMR method Beagle - SHAPEIT 0 -0.0006436 4.21e-05 1194 -15.2815689 0.0000000 8
AMR method Eagle - SHAPEIT 0 -0.0006234 4.21e-05 1194 -14.8018156 0.0000000 8
EAS method Beagle - Eagle 0 -0.0001358 5.81e-05 1194 -2.3378961 0.0511116 8
EAS method Beagle - SHAPEIT 0 -0.0004508 5.81e-05 1194 -7.7595044 0.0000000 8
EAS method Eagle - SHAPEIT 0 -0.0003150 5.81e-05 1194 -5.4216082 0.0000002 8
EUR method Beagle - Eagle 0 -0.0000456 4.77e-05 1194 -0.9576612 0.6038381 8
EUR method Beagle - SHAPEIT 0 -0.0003383 4.77e-05 1194 -7.0978298 0.0000000 8
EUR method Eagle - SHAPEIT 0 -0.0002926 4.77e-05 1194 -6.1401686 0.0000000 8
SAS method Beagle - Eagle 0 0.0001073 5.35e-05 1194 2.0074336 0.1108289 8
SAS method Beagle - SHAPEIT 0 -0.0006462 5.35e-05 1194 -12.0846881 0.0000000 8
SAS method Eagle - SHAPEIT 0 -0.0007535 5.35e-05 1194 -14.0921217 0.0000000 8
AFR method Beagle - Eagle 0 0.0005048 3.23e-05 1194 15.6450576 0.0000000 9
AFR method Beagle - SHAPEIT 0 -0.0004004 3.23e-05 1194 -12.4092070 0.0000000 9
AFR method Eagle - SHAPEIT 0 -0.0009052 3.23e-05 1194 -28.0542646 0.0000000 9
AMR method Beagle - Eagle 0 0.0000480 3.91e-05 1194 1.2283880 0.4365983 9
AMR method Beagle - SHAPEIT 0 -0.0005687 3.91e-05 1194 -14.5519496 0.0000000 9
AMR method Eagle - SHAPEIT 0 -0.0006168 3.91e-05 1194 -15.7803376 0.0000000 9
EAS method Beagle - Eagle 0 -0.0002605 5.39e-05 1194 -4.8323648 0.0000046 9
EAS method Beagle - SHAPEIT 0 -0.0005420 5.39e-05 1194 -10.0524216 0.0000000 9
EAS method Eagle - SHAPEIT 0 -0.0002814 5.39e-05 1194 -5.2200568 0.0000006 9
EUR method Beagle - Eagle 0 -0.0000072 4.42e-05 1194 -0.1623164 0.9855803 9
EUR method Beagle - SHAPEIT 0 -0.0002646 4.42e-05 1194 -5.9827613 0.0000000 9
EUR method Eagle - SHAPEIT 0 -0.0002574 4.42e-05 1194 -5.8204448 0.0000000 9
SAS method Beagle - Eagle 0 0.0001511 4.96e-05 1194 3.0445454 0.0067259 9
SAS method Beagle - SHAPEIT 0 -0.0006127 4.96e-05 1194 -12.3486181 0.0000000 9
SAS method Eagle - SHAPEIT 0 -0.0007638 4.96e-05 1194 -15.3931635 0.0000000 9
AFR method Beagle - Eagle 0 0.0004400 2.97e-05 1194 14.8217605 0.0000000 10
AFR method Beagle - SHAPEIT 0 -0.0003707 2.97e-05 1194 -12.4868312 0.0000000 10
AFR method Eagle - SHAPEIT 0 -0.0008108 2.97e-05 1194 -27.3085918 0.0000000 10
AMR method Beagle - Eagle 0 0.0000027 3.60e-05 1194 0.0763676 0.9967899 10
AMR method Beagle - SHAPEIT 0 -0.0004847 3.60e-05 1194 -13.4772797 0.0000000 10
AMR method Eagle - SHAPEIT 0 -0.0004874 3.60e-05 1194 -13.5536472 0.0000000 10
EAS method Beagle - Eagle 0 -0.0002428 4.96e-05 1194 -4.8937123 0.0000034 10
EAS method Beagle - SHAPEIT 0 -0.0005918 4.96e-05 1194 -11.9304773 0.0000000 10
EAS method Eagle - SHAPEIT 0 -0.0003491 4.96e-05 1194 -7.0367650 0.0000000 10
EUR method Beagle - Eagle 0 -0.0000309 4.07e-05 1194 -0.7583770 0.7286062 10
EUR method Beagle - SHAPEIT 0 -0.0002610 4.07e-05 1194 -6.4133877 0.0000000 10
EUR method Eagle - SHAPEIT 0 -0.0002301 4.07e-05 1194 -5.6550107 0.0000001 10
SAS method Beagle - Eagle 0 -0.0000379 4.57e-05 1194 -0.8296017 0.6846975 10
SAS method Beagle - SHAPEIT 0 -0.0006058 4.57e-05 1194 -13.2696823 0.0000000 10
SAS method Eagle - SHAPEIT 0 -0.0005679 4.57e-05 1194 -12.4400806 0.0000000 10
AFR method Beagle - Eagle 0 0.0004802 3.17e-05 1194 15.1488380 0.0000000 11
AFR method Beagle - SHAPEIT 0 -0.0004014 3.17e-05 1194 -12.6630091 0.0000000 11
AFR method Eagle - SHAPEIT 0 -0.0008817 3.17e-05 1194 -27.8118471 0.0000000 11
AMR method Beagle - Eagle 0 0.0000337 3.84e-05 1194 0.8768243 0.6550521 11
AMR method Beagle - SHAPEIT 0 -0.0004901 3.84e-05 1194 -12.7643833 0.0000000 11
AMR method Eagle - SHAPEIT 0 -0.0005238 3.84e-05 1194 -13.6412075 0.0000000 11
EAS method Beagle - Eagle 0 -0.0001510 5.30e-05 1194 -2.8508519 0.0123255 11
EAS method Beagle - SHAPEIT 0 -0.0005763 5.30e-05 1194 -10.8796391 0.0000000 11
EAS method Eagle - SHAPEIT 0 -0.0004253 5.30e-05 1194 -8.0287872 0.0000000 11
EUR method Beagle - Eagle 0 -0.0000828 4.34e-05 1194 -1.9064647 0.1372569 11
EUR method Beagle - SHAPEIT 0 -0.0002914 4.34e-05 1194 -6.7057425 0.0000000 11
EUR method Eagle - SHAPEIT 0 -0.0002085 4.34e-05 1194 -4.7992778 0.0000054 11
SAS method Beagle - Eagle 0 0.0000470 4.87e-05 1194 0.9641536 0.5997178 11
SAS method Beagle - SHAPEIT 0 -0.0005590 4.87e-05 1194 -11.4674726 0.0000000 11
SAS method Eagle - SHAPEIT 0 -0.0006060 4.87e-05 1194 -12.4316263 0.0000000 11
AFR method Beagle - Eagle 0 0.0005216 3.93e-05 1194 13.2622619 0.0000000 12
AFR method Beagle - SHAPEIT 0 -0.0003833 3.93e-05 1194 -9.7459948 0.0000000 12
AFR method Eagle - SHAPEIT 0 -0.0009050 3.93e-05 1194 -23.0082566 0.0000000 12
AMR method Beagle - Eagle 0 0.0000017 4.76e-05 1194 0.0347542 0.9993343 12
AMR method Beagle - SHAPEIT 0 -0.0005482 4.76e-05 1194 -11.5070928 0.0000000 12
AMR method Eagle - SHAPEIT 0 -0.0005499 4.76e-05 1194 -11.5418470 0.0000000 12
EAS method Beagle - Eagle 0 -0.0002102 6.57e-05 1194 -3.1985743 0.0040464 12
EAS method Beagle - SHAPEIT 0 -0.0006219 6.57e-05 1194 -9.4639273 0.0000000 12
EAS method Eagle - SHAPEIT 0 -0.0004117 6.57e-05 1194 -6.2653530 0.0000000 12
EUR method Beagle - Eagle 0 -0.0000254 5.39e-05 1194 -0.4711667 0.8848616 12
EUR method Beagle - SHAPEIT 0 -0.0003447 5.39e-05 1194 -6.3939818 0.0000000 12
EUR method Eagle - SHAPEIT 0 -0.0003193 5.39e-05 1194 -5.9228152 0.0000000 12
SAS method Beagle - Eagle 0 0.0002536 6.05e-05 1194 4.1928331 0.0000877 12
SAS method Beagle - SHAPEIT 0 -0.0007569 6.05e-05 1194 -12.5137184 0.0000000 12
SAS method Eagle - SHAPEIT 0 -0.0010105 6.05e-05 1194 -16.7065515 0.0000000 12
AFR method Beagle - Eagle 0 0.0005261 3.84e-05 1194 13.6934555 0.0000000 13
AFR method Beagle - SHAPEIT 0 -0.0003936 3.84e-05 1194 -10.2447170 0.0000000 13
AFR method Eagle - SHAPEIT 0 -0.0009197 3.84e-05 1194 -23.9381725 0.0000000 13
AMR method Beagle - Eagle 0 0.0000508 4.65e-05 1194 1.0915984 0.5194596 13
AMR method Beagle - SHAPEIT 0 -0.0005557 4.65e-05 1194 -11.9413517 0.0000000 13
AMR method Eagle - SHAPEIT 0 -0.0006065 4.65e-05 1194 -13.0329500 0.0000000 13
EAS method Beagle - Eagle 0 -0.0002402 6.42e-05 1194 -3.7413941 0.0005616 13
EAS method Beagle - SHAPEIT 0 -0.0005023 6.42e-05 1194 -7.8252429 0.0000000 13
EAS method Eagle - SHAPEIT 0 -0.0002622 6.42e-05 1194 -4.0838488 0.0001397 13
EUR method Beagle - Eagle 0 -0.0000228 5.27e-05 1194 -0.4331872 0.9017594 13
EUR method Beagle - SHAPEIT 0 -0.0002979 5.27e-05 1194 -5.6572024 0.0000001 13
EUR method Eagle - SHAPEIT 0 -0.0002751 5.27e-05 1194 -5.2240152 0.0000006 13
SAS method Beagle - Eagle 0 -0.0002002 5.91e-05 1194 -3.3883083 0.0020959 13
SAS method Beagle - SHAPEIT 0 -0.0007263 5.91e-05 1194 -12.2937546 0.0000000 13
SAS method Eagle - SHAPEIT 0 -0.0005262 5.91e-05 1194 -8.9054463 0.0000000 13
AFR method Beagle - Eagle 0 0.0004452 3.62e-05 1194 12.3085578 0.0000000 14
AFR method Beagle - SHAPEIT 0 -0.0004266 3.62e-05 1194 -11.7920322 0.0000000 14
AFR method Eagle - SHAPEIT 0 -0.0008718 3.62e-05 1194 -24.1005900 0.0000000 14
AMR method Beagle - Eagle 0 -0.0000236 4.38e-05 1194 -0.5377136 0.8527486 14
AMR method Beagle - SHAPEIT 0 -0.0005755 4.38e-05 1194 -13.1343977 0.0000000 14
AMR method Eagle - SHAPEIT 0 -0.0005519 4.38e-05 1194 -12.5966841 0.0000000 14
EAS method Beagle - Eagle 0 -0.0004212 6.04e-05 1194 -6.9683875 0.0000000 14
EAS method Beagle - SHAPEIT 0 -0.0006728 6.04e-05 1194 -11.1314465 0.0000000 14
EAS method Eagle - SHAPEIT 0 -0.0002516 6.04e-05 1194 -4.1630590 0.0000997 14
EUR method Beagle - Eagle 0 -0.0001347 4.96e-05 1194 -2.7177888 0.0182858 14
EUR method Beagle - SHAPEIT 0 -0.0004064 4.96e-05 1194 -8.1964235 0.0000000 14
EUR method Eagle - SHAPEIT 0 -0.0002716 4.96e-05 1194 -5.4786347 0.0000002 14
SAS method Beagle - Eagle 0 0.0000396 5.56e-05 1194 0.7124864 0.7561536 14
SAS method Beagle - SHAPEIT 0 -0.0006810 5.56e-05 1194 -12.2420022 0.0000000 14
SAS method Eagle - SHAPEIT 0 -0.0007206 5.56e-05 1194 -12.9544886 0.0000000 14
AFR method Beagle - Eagle 0 0.0003587 3.80e-05 1194 9.4386505 0.0000000 15
AFR method Beagle - SHAPEIT 0 -0.0003949 3.80e-05 1194 -10.3903120 0.0000000 15
AFR method Eagle - SHAPEIT 0 -0.0007536 3.80e-05 1194 -19.8289624 0.0000000 15
AMR method Beagle - Eagle 0 -0.0000228 4.60e-05 1194 -0.4962488 0.8731169 15
AMR method Beagle - SHAPEIT 0 -0.0006085 4.60e-05 1194 -13.2192618 0.0000000 15
AMR method Eagle - SHAPEIT 0 -0.0005857 4.60e-05 1194 -12.7230130 0.0000000 15
EAS method Beagle - Eagle 0 -0.0002662 6.35e-05 1194 -4.1924257 0.0000878 15
EAS method Beagle - SHAPEIT 0 -0.0006438 6.35e-05 1194 -10.1394519 0.0000000 15
EAS method Eagle - SHAPEIT 0 -0.0003776 6.35e-05 1194 -5.9470262 0.0000000 15
EUR method Beagle - Eagle 0 -0.0000594 5.21e-05 1194 -1.1409907 0.4890059 15
EUR method Beagle - SHAPEIT 0 -0.0003142 5.21e-05 1194 -6.0314706 0.0000000 15
EUR method Eagle - SHAPEIT 0 -0.0002547 5.21e-05 1194 -4.8904799 0.0000034 15
SAS method Beagle - Eagle 0 -0.0001424 5.84e-05 1194 -2.4374077 0.0396042 15
SAS method Beagle - SHAPEIT 0 -0.0008296 5.84e-05 1194 -14.1949264 0.0000000 15
SAS method Eagle - SHAPEIT 0 -0.0006871 5.84e-05 1194 -11.7575187 0.0000000 15
AFR method Beagle - Eagle 0 0.0003689 4.77e-05 1194 7.7338629 0.0000000 16
AFR method Beagle - SHAPEIT 0 -0.0003993 4.77e-05 1194 -8.3715322 0.0000000 16
AFR method Eagle - SHAPEIT 0 -0.0007682 4.77e-05 1194 -16.1053950 0.0000000 16
AMR method Beagle - Eagle 0 0.0000565 5.78e-05 1194 0.9779683 0.5909538 16
AMR method Beagle - SHAPEIT 0 -0.0006281 5.78e-05 1194 -10.8712620 0.0000000 16
AMR method Eagle - SHAPEIT 0 -0.0006846 5.78e-05 1194 -11.8492303 0.0000000 16
EAS method Beagle - Eagle 0 -0.0002005 7.97e-05 1194 -2.5156145 0.0321812 16
EAS method Beagle - SHAPEIT 0 -0.0006164 7.97e-05 1194 -7.7342443 0.0000000 16
EAS method Eagle - SHAPEIT 0 -0.0004159 7.97e-05 1194 -5.2186298 0.0000006 16
EUR method Beagle - Eagle 0 -0.0002904 6.54e-05 1194 -4.4419836 0.0000290 16
EUR method Beagle - SHAPEIT 0 -0.0006080 6.54e-05 1194 -9.2998373 0.0000000 16
EUR method Eagle - SHAPEIT 0 -0.0003176 6.54e-05 1194 -4.8578538 0.0000040 16
SAS method Beagle - Eagle 0 0.0004022 7.33e-05 1194 5.4832923 0.0000002 16
SAS method Beagle - SHAPEIT 0 -0.0005987 7.33e-05 1194 -8.1627773 0.0000000 16
SAS method Eagle - SHAPEIT 0 -0.0010009 7.33e-05 1194 -13.6460695 0.0000000 16
AFR method Beagle - Eagle 0 0.0002622 4.38e-05 1194 5.9858512 0.0000000 17
AFR method Beagle - SHAPEIT 0 -0.0004987 4.38e-05 1194 -11.3826610 0.0000000 17
AFR method Eagle - SHAPEIT 0 -0.0007609 4.38e-05 1194 -17.3685122 0.0000000 17
AMR method Beagle - Eagle 0 -0.0000364 5.31e-05 1194 -0.6852430 0.7721556 17
AMR method Beagle - SHAPEIT 0 -0.0005208 5.31e-05 1194 -9.8149434 0.0000000 17
AMR method Eagle - SHAPEIT 0 -0.0004845 5.31e-05 1194 -9.1297004 0.0000000 17
EAS method Beagle - Eagle 0 -0.0002022 7.32e-05 1194 -2.7617166 0.0160847 17
EAS method Beagle - SHAPEIT 0 -0.0005352 7.32e-05 1194 -7.3110209 0.0000000 17
EAS method Eagle - SHAPEIT 0 -0.0003330 7.32e-05 1194 -4.5493043 0.0000177 17
EUR method Beagle - Eagle 0 -0.0001355 6.00e-05 1194 -2.2565365 0.0624910 17
EUR method Beagle - SHAPEIT 0 -0.0003435 6.00e-05 1194 -5.7210562 0.0000000 17
EUR method Eagle - SHAPEIT 0 -0.0002080 6.00e-05 1194 -3.4645197 0.0015934 17
SAS method Beagle - Eagle 0 -0.0001435 6.74e-05 1194 -2.1304709 0.0841853 17
SAS method Beagle - SHAPEIT 0 -0.0006087 6.74e-05 1194 -9.0352654 0.0000000 17
SAS method Eagle - SHAPEIT 0 -0.0004652 6.74e-05 1194 -6.9047945 0.0000000 17
AFR method Beagle - Eagle 0 0.0004286 3.54e-05 1194 12.1029163 0.0000000 18
AFR method Beagle - SHAPEIT 0 -0.0004583 3.54e-05 1194 -12.9413121 0.0000000 18
AFR method Eagle - SHAPEIT 0 -0.0008869 3.54e-05 1194 -25.0442284 0.0000000 18
AMR method Beagle - Eagle 0 0.0000538 4.29e-05 1194 1.2552844 0.4209309 18
AMR method Beagle - SHAPEIT 0 -0.0005582 4.29e-05 1194 -13.0135443 0.0000000 18
AMR method Eagle - SHAPEIT 0 -0.0006121 4.29e-05 1194 -14.2688287 0.0000000 18
EAS method Beagle - Eagle 0 -0.0002549 5.92e-05 1194 -4.3080744 0.0000529 18
EAS method Beagle - SHAPEIT 0 -0.0005295 5.92e-05 1194 -8.9482588 0.0000000 18
EAS method Eagle - SHAPEIT 0 -0.0002746 5.92e-05 1194 -4.6401844 0.0000115 18
EUR method Beagle - Eagle 0 -0.0001363 4.85e-05 1194 -2.8088141 0.0139881 18
EUR method Beagle - SHAPEIT 0 -0.0003425 4.85e-05 1194 -7.0553912 0.0000000 18
EUR method Eagle - SHAPEIT 0 -0.0002061 4.85e-05 1194 -4.2465772 0.0000694 18
SAS method Beagle - Eagle 0 0.0000726 5.45e-05 1194 1.3331711 0.3770016 18
SAS method Beagle - SHAPEIT 0 -0.0006050 5.45e-05 1194 -11.1083313 0.0000000 18
SAS method Eagle - SHAPEIT 0 -0.0006776 5.45e-05 1194 -12.4415024 0.0000000 18
AFR method Beagle - Eagle 0 0.0003216 4.30e-05 1194 7.4813169 0.0000000 19
AFR method Beagle - SHAPEIT 0 -0.0003063 4.30e-05 1194 -7.1249908 0.0000000 19
AFR method Eagle - SHAPEIT 0 -0.0006280 4.30e-05 1194 -14.6063077 0.0000000 19
AMR method Beagle - Eagle 0 -0.0000811 5.21e-05 1194 -1.5577378 0.2645574 19
AMR method Beagle - SHAPEIT 0 -0.0004183 5.21e-05 1194 -8.0328288 0.0000000 19
AMR method Eagle - SHAPEIT 0 -0.0003372 5.21e-05 1194 -6.4750909 0.0000000 19
EAS method Beagle - Eagle 0 -0.0001522 7.18e-05 1194 -2.1189795 0.0864328 19
EAS method Beagle - SHAPEIT 0 -0.0005116 7.18e-05 1194 -7.1215054 0.0000000 19
EAS method Eagle - SHAPEIT 0 -0.0003593 7.18e-05 1194 -5.0025259 0.0000019 19
EUR method Beagle - Eagle 0 -0.0000906 5.89e-05 1194 -1.5378709 0.2735718 19
EUR method Beagle - SHAPEIT 0 -0.0002416 5.89e-05 1194 -4.1009873 0.0001299 19
EUR method Eagle - SHAPEIT 0 -0.0001510 5.89e-05 1194 -2.5631163 0.0282837 19
SAS method Beagle - Eagle 0 0.0000927 6.61e-05 1194 1.4019229 0.3402032 19
SAS method Beagle - SHAPEIT 0 -0.0006045 6.61e-05 1194 -9.1442675 0.0000000 19
SAS method Eagle - SHAPEIT 0 -0.0006972 6.61e-05 1194 -10.5461904 0.0000000 19
AFR method Beagle - Eagle 0 0.0003607 4.12e-05 1194 8.7486537 0.0000000 20
AFR method Beagle - SHAPEIT 0 -0.0003029 4.12e-05 1194 -7.3462005 0.0000000 20
AFR method Eagle - SHAPEIT 0 -0.0006636 4.12e-05 1194 -16.0948542 0.0000000 20
AMR method Beagle - Eagle 0 -0.0000567 4.99e-05 1194 -1.1358979 0.4921217 20
AMR method Beagle - SHAPEIT 0 -0.0005121 4.99e-05 1194 -10.2540553 0.0000000 20
AMR method Eagle - SHAPEIT 0 -0.0004554 4.99e-05 1194 -9.1181574 0.0000000 20
EAS method Beagle - Eagle 0 -0.0002879 6.89e-05 1194 -4.1788964 0.0000931 20
EAS method Beagle - SHAPEIT 0 -0.0005742 6.89e-05 1194 -8.3355057 0.0000000 20
EAS method Eagle - SHAPEIT 0 -0.0002863 6.89e-05 1194 -4.1566093 0.0001025 20
EUR method Beagle - Eagle 0 -0.0001733 5.65e-05 1194 -3.0673045 0.0062486 20
EUR method Beagle - SHAPEIT 0 -0.0003020 5.65e-05 1194 -5.3445971 0.0000003 20
EUR method Eagle - SHAPEIT 0 -0.0001287 5.65e-05 1194 -2.2772926 0.0594055 20
SAS method Beagle - Eagle 0 0.0000269 6.34e-05 1194 0.4249621 0.9052721 20
SAS method Beagle - SHAPEIT 0 -0.0005352 6.34e-05 1194 -8.4418609 0.0000000 20
SAS method Eagle - SHAPEIT 0 -0.0005622 6.34e-05 1194 -8.8668230 0.0000000 20
AFR method Beagle - Eagle 0 0.0003008 4.79e-05 1194 6.2726141 0.0000000 21
AFR method Beagle - SHAPEIT 0 -0.0004479 4.79e-05 1194 -9.3411600 0.0000000 21
AFR method Eagle - SHAPEIT 0 -0.0007487 4.79e-05 1194 -15.6137740 0.0000000 21
AMR method Beagle - Eagle 0 -0.0001152 5.81e-05 1194 -1.9843647 0.1164881 21
AMR method Beagle - SHAPEIT 0 -0.0006034 5.81e-05 1194 -10.3886910 0.0000000 21
AMR method Eagle - SHAPEIT 0 -0.0004881 5.81e-05 1194 -8.4043262 0.0000000 21
EAS method Beagle - Eagle 0 -0.0002090 8.01e-05 1194 -2.6088978 0.0249208 21
EAS method Beagle - SHAPEIT 0 -0.0004776 8.01e-05 1194 -5.9608976 0.0000000 21
EAS method Eagle - SHAPEIT 0 -0.0002685 8.01e-05 1194 -3.3519998 0.0023836 21
EUR method Beagle - Eagle 0 -0.0001388 6.57e-05 1194 -2.1114952 0.0879222 21
EUR method Beagle - SHAPEIT 0 -0.0004037 6.57e-05 1194 -6.1423595 0.0000000 21
EUR method Eagle - SHAPEIT 0 -0.0002649 6.57e-05 1194 -4.0308643 0.0001745 21
SAS method Beagle - Eagle 0 -0.0000789 7.37e-05 1194 -1.0696380 0.5331493 21
SAS method Beagle - SHAPEIT 0 -0.0006798 7.37e-05 1194 -9.2191316 0.0000000 21
SAS method Eagle - SHAPEIT 0 -0.0006009 7.37e-05 1194 -8.1494936 0.0000000 21
AFR method Beagle - Eagle 0 0.0001776 5.35e-05 1194 3.3221526 0.0026468 22
AFR method Beagle - SHAPEIT 0 -0.0003215 5.35e-05 1194 -6.0125758 0.0000000 22
AFR method Eagle - SHAPEIT 0 -0.0004991 5.35e-05 1194 -9.3347284 0.0000000 22
AMR method Beagle - Eagle 0 -0.0001744 6.48e-05 1194 -2.6923316 0.0196794 22
AMR method Beagle - SHAPEIT 0 -0.0004658 6.48e-05 1194 -7.1925821 0.0000000 22
AMR method Eagle - SHAPEIT 0 -0.0002914 6.48e-05 1194 -4.5002504 0.0000222 22
EAS method Beagle - Eagle 0 -0.0004043 8.93e-05 1194 -4.5254701 0.0000197 22
EAS method Beagle - SHAPEIT 0 -0.0004010 8.93e-05 1194 -4.4883624 0.0000234 22
EAS method Eagle - SHAPEIT 0 0.0000033 8.93e-05 1194 0.0371077 0.9992411 22
EUR method Beagle - Eagle 0 -0.0001993 7.33e-05 1194 -2.7191826 0.0182121 22
EUR method Beagle - SHAPEIT 0 -0.0003548 7.33e-05 1194 -4.8410279 0.0000044 22
EUR method Eagle - SHAPEIT 0 -0.0001555 7.33e-05 1194 -2.1218453 0.0858678 22
SAS method Beagle - Eagle 0 -0.0001315 8.22e-05 1194 -1.5988523 0.2465055 22
SAS method Beagle - SHAPEIT 0 -0.0006356 8.22e-05 1194 -7.7299990 0.0000000 22
SAS method Eagle - SHAPEIT 0 -0.0005041 8.22e-05 1194 -6.1311467 0.0000000 22
AFR method Beagle - Eagle 0 -0.0004588 1.80e-05 1990 -25.4372255 0.0000000 23
AFR method Beagle - SHAPEIT 0 -0.0000692 1.80e-05 1990 -3.8350570 0.0003805 23
AFR method Eagle - SHAPEIT 0 0.0003896 1.80e-05 1990 21.6021685 0.0000000 23
AMR method Beagle - Eagle 0 -0.0004346 1.80e-05 1990 -24.0941650 0.0000000 23
AMR method Beagle - SHAPEIT 0 -0.0000927 1.80e-05 1990 -5.1416197 0.0000009 23
AMR method Eagle - SHAPEIT 0 0.0003418 1.80e-05 1990 18.9525452 0.0000000 23
EAS method Beagle - Eagle 0 -0.0008134 1.80e-05 1990 -45.0949894 0.0000000 23
EAS method Beagle - SHAPEIT 0 0.0000256 1.80e-05 1990 1.4204075 0.3305162 23
EAS method Eagle - SHAPEIT 0 0.0008390 1.80e-05 1990 46.5153968 0.0000000 23
EUR method Beagle - Eagle 0 -0.0005408 1.80e-05 1990 -29.9828894 0.0000000 23
EUR method Beagle - SHAPEIT 0 -0.0000649 1.80e-05 1990 -3.5966972 0.0009624 23
EUR method Eagle - SHAPEIT 0 0.0004759 1.80e-05 1990 26.3861922 0.0000000 23
SAS method Beagle - Eagle 0 -0.0006780 1.80e-05 1990 -37.5903655 0.0000000 23
SAS method Beagle - SHAPEIT 0 -0.0000273 1.80e-05 1990 -1.5111478 0.2858440 23
SAS method Eagle - SHAPEIT 0 0.0006508 1.80e-05 1990 36.0792178 0.0000000 23
df_pop_pop %>% knitr::kable()
method term contrast null.value estimate std.error df statistic adj.p.value chrom
Beagle SUPER AFR - AMR 0 -0.0012125 0.0001918 616.1882 -6.3226634 0.0000000 1
Beagle SUPER AFR - EAS 0 -0.0045375 0.0002377 616.1882 -19.0863327 0.0000000 1
Beagle SUPER AFR - EUR 0 -0.0010421 0.0002071 616.1882 -5.0308144 0.0000064 1
Beagle SUPER AFR - SAS 0 -0.0034997 0.0002240 616.1882 -15.6273412 0.0000000 1
Beagle SUPER AMR - EAS 0 -0.0033250 0.0002520 616.1882 -13.1968292 0.0000000 1
Beagle SUPER AMR - EUR 0 0.0001704 0.0002233 616.1882 0.7630794 0.9410205 1
Beagle SUPER AMR - SAS 0 -0.0022873 0.0002390 616.1882 -9.5704702 0.0000000 1
Beagle SUPER EAS - EUR 0 0.0034954 0.0002638 616.1882 13.2481109 0.0000000 1
Beagle SUPER EAS - SAS 0 0.0010377 0.0002772 616.1882 3.7431667 0.0018528 1
Beagle SUPER EUR - SAS 0 -0.0024577 0.0002515 616.1882 -9.7723339 0.0000000 1
Eagle SUPER AFR - AMR 0 -0.0016806 0.0001918 616.1882 -8.7639580 0.0000000 1
Eagle SUPER AFR - EAS 0 -0.0052678 0.0002377 616.1882 -22.1580917 0.0000000 1
Eagle SUPER AFR - EUR 0 -0.0015956 0.0002071 616.1882 -7.7030756 0.0000000 1
Eagle SUPER AFR - SAS 0 -0.0039263 0.0002240 616.1882 -17.5320761 0.0000000 1
Eagle SUPER AMR - EAS 0 -0.0035871 0.0002520 616.1882 -14.2371048 0.0000000 1
Eagle SUPER AMR - EUR 0 0.0000850 0.0002233 616.1882 0.3808090 0.9955331 1
Eagle SUPER AMR - SAS 0 -0.0022457 0.0002390 616.1882 -9.3964212 0.0000000 1
Eagle SUPER EAS - EUR 0 0.0036721 0.0002638 616.1882 13.9179639 0.0000000 1
Eagle SUPER EAS - SAS 0 0.0013414 0.0002772 616.1882 4.8386172 0.0000163 1
Eagle SUPER EUR - SAS 0 -0.0023307 0.0002515 616.1882 -9.2674955 0.0000000 1
SHAPEIT SUPER AFR - AMR 0 -0.0013815 0.0001918 616.1882 -7.2039711 0.0000000 1
SHAPEIT SUPER AFR - EAS 0 -0.0047098 0.0002377 616.1882 -19.8111881 0.0000000 1
SHAPEIT SUPER AFR - EUR 0 -0.0009697 0.0002071 616.1882 -4.6811806 0.0000345 1
SHAPEIT SUPER AFR - SAS 0 -0.0037750 0.0002240 616.1882 -16.8565374 0.0000000 1
SHAPEIT SUPER AMR - EAS 0 -0.0033283 0.0002520 616.1882 -13.2099938 0.0000000 1
SHAPEIT SUPER AMR - EUR 0 0.0004118 0.0002233 616.1882 1.8441927 0.3491025 1
SHAPEIT SUPER AMR - SAS 0 -0.0023935 0.0002390 616.1882 -10.0151392 0.0000000 1
SHAPEIT SUPER EAS - EUR 0 0.0037402 0.0002638 616.1882 14.1757339 0.0000000 1
SHAPEIT SUPER EAS - SAS 0 0.0009348 0.0002772 616.1882 3.3718037 0.0070774 1
SHAPEIT SUPER EUR - SAS 0 -0.0028054 0.0002515 616.1882 -11.1548852 0.0000000 1
Beagle SUPER AFR - AMR 0 -0.0014510 0.0001893 618.2141 -7.6661287 0.0000000 2
Beagle SUPER AFR - EAS 0 -0.0045791 0.0002346 618.2141 -19.5149909 0.0000000 2
Beagle SUPER AFR - EUR 0 -0.0008447 0.0002044 618.2141 -4.1317571 0.0003933 2
Beagle SUPER AFR - SAS 0 -0.0035259 0.0002210 618.2141 -15.9513954 0.0000000 2
Beagle SUPER AMR - EAS 0 -0.0031281 0.0002487 618.2141 -12.5787557 0.0000000 2
Beagle SUPER AMR - EUR 0 0.0006063 0.0002204 618.2141 2.7506861 0.0480162 2
Beagle SUPER AMR - SAS 0 -0.0020749 0.0002359 618.2141 -8.7961269 0.0000000 2
Beagle SUPER EAS - EUR 0 0.0037344 0.0002604 618.2141 14.3401901 0.0000000 2
Beagle SUPER EAS - SAS 0 0.0010532 0.0002736 618.2141 3.8489790 0.0012325 2
Beagle SUPER EUR - SAS 0 -0.0026812 0.0002482 618.2141 -10.8013964 0.0000000 2
Eagle SUPER AFR - AMR 0 -0.0018796 0.0001893 618.2141 -9.9307186 0.0000000 2
Eagle SUPER AFR - EAS 0 -0.0052680 0.0002346 618.2141 -22.4507941 0.0000000 2
Eagle SUPER AFR - EUR 0 -0.0013335 0.0002044 618.2141 -6.5223458 0.0000000 2
Eagle SUPER AFR - SAS 0 -0.0038909 0.0002210 618.2141 -17.6026197 0.0000000 2
Eagle SUPER AMR - EAS 0 -0.0033883 0.0002487 618.2141 -13.6252422 0.0000000 2
Eagle SUPER AMR - EUR 0 0.0005462 0.0002204 618.2141 2.4779423 0.0969742 2
Eagle SUPER AMR - SAS 0 -0.0020112 0.0002359 618.2141 -8.5263112 0.0000000 2
Eagle SUPER EAS - EUR 0 0.0039345 0.0002604 618.2141 15.1086773 0.0000000 2
Eagle SUPER EAS - SAS 0 0.0013771 0.0002736 618.2141 5.0326298 0.0000063 2
Eagle SUPER EUR - SAS 0 -0.0025574 0.0002482 618.2141 -10.3028069 0.0000000 2
SHAPEIT SUPER AFR - AMR 0 -0.0015523 0.0001893 618.2141 -8.2014905 0.0000000 2
SHAPEIT SUPER AFR - EAS 0 -0.0048366 0.0002346 618.2141 -20.6124634 0.0000000 2
SHAPEIT SUPER AFR - EUR 0 -0.0007976 0.0002044 618.2141 -3.9013075 0.0010036 2
SHAPEIT SUPER AFR - SAS 0 -0.0037531 0.0002210 618.2141 -16.9793542 0.0000000 2
SHAPEIT SUPER AMR - EAS 0 -0.0032843 0.0002487 618.2141 -13.2068142 0.0000000 2
SHAPEIT SUPER AMR - EUR 0 0.0007547 0.0002204 618.2141 3.4241741 0.0059079 2
SHAPEIT SUPER AMR - SAS 0 -0.0022008 0.0002359 618.2141 -9.3298123 0.0000000 2
SHAPEIT SUPER EAS - EUR 0 0.0040390 0.0002604 618.2141 15.5099899 0.0000000 2
SHAPEIT SUPER EAS - SAS 0 0.0010835 0.0002736 618.2141 3.9597004 0.0007954 2
SHAPEIT SUPER EUR - SAS 0 -0.0029555 0.0002482 618.2141 -11.9065845 0.0000000 2
Beagle SUPER AFR - AMR 0 -0.0012736 0.0001824 618.4175 -6.9842973 0.0000000 3
Beagle SUPER AFR - EAS 0 -0.0042897 0.0002261 618.4175 -18.9757873 0.0000000 3
Beagle SUPER AFR - EUR 0 -0.0010075 0.0001970 618.4175 -5.1150992 0.0000042 3
Beagle SUPER AFR - SAS 0 -0.0032765 0.0002130 618.4175 -15.3859277 0.0000000 3
Beagle SUPER AMR - EAS 0 -0.0030161 0.0002396 618.4175 -12.5889395 0.0000000 3
Beagle SUPER AMR - EUR 0 0.0002661 0.0002124 618.4175 1.2530659 0.7200460 3
Beagle SUPER AMR - SAS 0 -0.0020029 0.0002273 618.4175 -8.8133525 0.0000000 3
Beagle SUPER EAS - EUR 0 0.0032822 0.0002509 618.4175 13.0823331 0.0000000 3
Beagle SUPER EAS - SAS 0 0.0010132 0.0002636 618.4175 3.8433848 0.0012597 3
Beagle SUPER EUR - SAS 0 -0.0022690 0.0002391 618.4175 -9.4879388 0.0000000 3
Eagle SUPER AFR - AMR 0 -0.0017058 0.0001824 618.4175 -9.3546293 0.0000000 3
Eagle SUPER AFR - EAS 0 -0.0050098 0.0002261 618.4175 -22.1612288 0.0000000 3
Eagle SUPER AFR - EUR 0 -0.0015409 0.0001970 618.4175 -7.8228288 0.0000000 3
Eagle SUPER AFR - SAS 0 -0.0036619 0.0002130 618.4175 -17.1955558 0.0000000 3
Eagle SUPER AMR - EAS 0 -0.0033040 0.0002396 618.4175 -13.7904928 0.0000000 3
Eagle SUPER AMR - EUR 0 0.0001650 0.0002124 618.4175 0.7769585 0.9372165 3
Eagle SUPER AMR - SAS 0 -0.0019560 0.0002273 618.4175 -8.6071232 0.0000000 3
Eagle SUPER EAS - EUR 0 0.0034690 0.0002509 618.4175 13.8267740 0.0000000 3
Eagle SUPER EAS - SAS 0 0.0013479 0.0002636 618.4175 5.1131469 0.0000042 3
Eagle SUPER EUR - SAS 0 -0.0021210 0.0002391 618.4175 -8.8691961 0.0000000 3
SHAPEIT SUPER AFR - AMR 0 -0.0013764 0.0001824 618.4175 -7.5481042 0.0000000 3
SHAPEIT SUPER AFR - EAS 0 -0.0044414 0.0002261 618.4175 -19.6467338 0.0000000 3
SHAPEIT SUPER AFR - EUR 0 -0.0009338 0.0001970 618.4175 -4.7407509 0.0000260 3
SHAPEIT SUPER AFR - SAS 0 -0.0035155 0.0002130 618.4175 -16.5081940 0.0000000 3
SHAPEIT SUPER AMR - EAS 0 -0.0030650 0.0002396 618.4175 -12.7928942 0.0000000 3
SHAPEIT SUPER AMR - EUR 0 0.0004426 0.0002124 618.4175 2.0844555 0.2280753 3
SHAPEIT SUPER AMR - SAS 0 -0.0021391 0.0002273 618.4175 -9.4125857 0.0000000 3
SHAPEIT SUPER EAS - EUR 0 0.0035076 0.0002509 618.4175 13.9807848 0.0000000 3
SHAPEIT SUPER EAS - SAS 0 0.0009259 0.0002636 618.4175 3.5121715 0.0043348 3
SHAPEIT SUPER EUR - SAS 0 -0.0025817 0.0002391 618.4175 -10.7956267 0.0000000 3
Beagle SUPER AFR - AMR 0 -0.0014318 0.0001666 624.9824 -8.5965559 0.0000000 4
Beagle SUPER AFR - EAS 0 -0.0037890 0.0002065 624.9824 -18.3502878 0.0000000 4
Beagle SUPER AFR - EUR 0 -0.0009205 0.0001799 624.9824 -5.1164543 0.0000041 4
Beagle SUPER AFR - SAS 0 -0.0032001 0.0001945 624.9824 -16.4523674 0.0000000 4
Beagle SUPER AMR - EAS 0 -0.0023572 0.0002188 624.9824 -10.7716189 0.0000000 4
Beagle SUPER AMR - EUR 0 0.0005113 0.0001940 624.9824 2.6363058 0.0651550 4
Beagle SUPER AMR - SAS 0 -0.0017683 0.0002076 624.9824 -8.5189904 0.0000000 4
Beagle SUPER EAS - EUR 0 0.0028685 0.0002292 624.9824 12.5176632 0.0000000 4
Beagle SUPER EAS - SAS 0 0.0005889 0.0002408 624.9824 2.4455429 0.1047865 4
Beagle SUPER EUR - SAS 0 -0.0022796 0.0002184 624.9824 -10.4364704 0.0000000 4
Eagle SUPER AFR - AMR 0 -0.0019050 0.0001666 624.9824 -11.4375177 0.0000000 4
Eagle SUPER AFR - EAS 0 -0.0045719 0.0002065 624.9824 -22.1423035 0.0000000 4
Eagle SUPER AFR - EUR 0 -0.0014509 0.0001799 624.9824 -8.0648147 0.0000000 4
Eagle SUPER AFR - SAS 0 -0.0035637 0.0001945 624.9824 -18.3216285 0.0000000 4
Eagle SUPER AMR - EAS 0 -0.0026670 0.0002188 624.9824 -12.1873065 0.0000000 4
Eagle SUPER AMR - EUR 0 0.0004541 0.0001940 624.9824 2.3411432 0.1334060 4
Eagle SUPER AMR - SAS 0 -0.0016587 0.0002076 624.9824 -7.9910055 0.0000000 4
Eagle SUPER EAS - EUR 0 0.0031210 0.0002292 624.9824 13.6197417 0.0000000 4
Eagle SUPER EAS - SAS 0 0.0010082 0.0002408 624.9824 4.1872818 0.0003111 4
Eagle SUPER EUR - SAS 0 -0.0021128 0.0002184 624.9824 -9.6726375 0.0000000 4
SHAPEIT SUPER AFR - AMR 0 -0.0016079 0.0001666 624.9824 -9.6535308 0.0000000 4
SHAPEIT SUPER AFR - EAS 0 -0.0041110 0.0002065 624.9824 -19.9097927 0.0000000 4
SHAPEIT SUPER AFR - EUR 0 -0.0009016 0.0001799 624.9824 -5.0112483 0.0000070 4
SHAPEIT SUPER AFR - SAS 0 -0.0033882 0.0001945 624.9824 -17.4191854 0.0000000 4
SHAPEIT SUPER AMR - EAS 0 -0.0025031 0.0002188 624.9824 -11.4386233 0.0000000 4
SHAPEIT SUPER AMR - EUR 0 0.0007063 0.0001940 624.9824 3.6415483 0.0027082 4
SHAPEIT SUPER AMR - SAS 0 -0.0017803 0.0002076 624.9824 -8.5768384 0.0000000 4
SHAPEIT SUPER EAS - EUR 0 0.0032094 0.0002292 624.9824 14.0054502 0.0000000 4
SHAPEIT SUPER EAS - SAS 0 0.0007228 0.0002408 624.9824 3.0018544 0.0232890 4
SHAPEIT SUPER EUR - SAS 0 -0.0024866 0.0002184 624.9824 -11.3840583 0.0000000 4
Beagle SUPER AFR - AMR 0 -0.0011335 0.0001901 618.6204 -5.9628756 0.0000000 5
Beagle SUPER AFR - EAS 0 -0.0042093 0.0002357 618.6204 -17.8622579 0.0000000 5
Beagle SUPER AFR - EUR 0 -0.0008796 0.0002053 618.6204 -4.2837826 0.0002062 5
Beagle SUPER AFR - SAS 0 -0.0034256 0.0002220 618.6204 -15.4310327 0.0000000 5
Beagle SUPER AMR - EAS 0 -0.0030759 0.0002498 618.6204 -12.3156806 0.0000000 5
Beagle SUPER AMR - EUR 0 0.0002539 0.0002214 618.6204 1.1470363 0.7813251 5
Beagle SUPER AMR - SAS 0 -0.0022921 0.0002369 618.6204 -9.6752120 0.0000000 5
Beagle SUPER EAS - EUR 0 0.0033298 0.0002615 618.6204 12.7316428 0.0000000 5
Beagle SUPER EAS - SAS 0 0.0007838 0.0002748 618.6204 2.8520784 0.0361675 5
Beagle SUPER EUR - SAS 0 -0.0025460 0.0002493 618.6204 -10.2128077 0.0000000 5
Eagle SUPER AFR - AMR 0 -0.0016400 0.0001901 618.6204 -8.6273259 0.0000000 5
Eagle SUPER AFR - EAS 0 -0.0049081 0.0002357 618.6204 -20.8273037 0.0000000 5
Eagle SUPER AFR - EUR 0 -0.0014142 0.0002053 618.6204 -6.8874783 0.0000000 5
Eagle SUPER AFR - SAS 0 -0.0038121 0.0002220 618.6204 -17.1721184 0.0000000 5
Eagle SUPER AMR - EAS 0 -0.0032681 0.0002498 618.6204 -13.0854173 0.0000000 5
Eagle SUPER AMR - EUR 0 0.0002258 0.0002214 618.6204 1.0199953 0.8461585 5
Eagle SUPER AMR - SAS 0 -0.0021721 0.0002369 618.6204 -9.1687524 0.0000000 5
Eagle SUPER EAS - EUR 0 0.0034939 0.0002615 618.6204 13.3591717 0.0000000 5
Eagle SUPER EAS - SAS 0 0.0010960 0.0002748 618.6204 3.9882156 0.0007091 5
Eagle SUPER EUR - SAS 0 -0.0023979 0.0002493 618.6204 -9.6187154 0.0000000 5
SHAPEIT SUPER AFR - AMR 0 -0.0013544 0.0001901 618.6204 -7.1248035 0.0000000 5
SHAPEIT SUPER AFR - EAS 0 -0.0044883 0.0002357 618.6204 -19.0460952 0.0000000 5
SHAPEIT SUPER AFR - EUR 0 -0.0008256 0.0002053 618.6204 -4.0207336 0.0006216 5
SHAPEIT SUPER AFR - SAS 0 -0.0036648 0.0002220 618.6204 -16.5087887 0.0000000 5
SHAPEIT SUPER AMR - EAS 0 -0.0031340 0.0002498 618.6204 -12.5483373 0.0000000 5
SHAPEIT SUPER AMR - EUR 0 0.0005288 0.0002214 618.6204 2.3888142 0.1196902 5
SHAPEIT SUPER AMR - SAS 0 -0.0023104 0.0002369 618.6204 -9.7528012 0.0000000 5
SHAPEIT SUPER EAS - EUR 0 0.0036627 0.0002615 618.6204 14.0048548 0.0000000 5
SHAPEIT SUPER EAS - SAS 0 0.0008235 0.0002748 618.6204 2.9966330 0.0236668 5
SHAPEIT SUPER EUR - SAS 0 -0.0028392 0.0002493 618.6204 -11.3891895 0.0000000 5
Beagle SUPER AFR - AMR 0 -0.0010278 0.0001689 619.7714 -6.0861081 0.0000000 6
Beagle SUPER AFR - EAS 0 -0.0036264 0.0002094 619.7714 -17.3206822 0.0000000 6
Beagle SUPER AFR - EUR 0 -0.0006144 0.0001824 619.7714 -3.3679924 0.0071679 6
Beagle SUPER AFR - SAS 0 -0.0029280 0.0001972 619.7714 -14.8459920 0.0000000 6
Beagle SUPER AMR - EAS 0 -0.0025985 0.0002219 619.7714 -11.7108756 0.0000000 6
Beagle SUPER AMR - EUR 0 0.0004135 0.0001967 619.7714 2.1023116 0.2203142 6
Beagle SUPER AMR - SAS 0 -0.0019002 0.0002105 619.7714 -9.0281098 0.0000000 6
Beagle SUPER EAS - EUR 0 0.0030120 0.0002324 619.7714 12.9626300 0.0000000 6
Beagle SUPER EAS - SAS 0 0.0006983 0.0002442 619.7714 2.8602610 0.0353300 6
Beagle SUPER EUR - SAS 0 -0.0023136 0.0002215 619.7714 -10.4461174 0.0000000 6
Eagle SUPER AFR - AMR 0 -0.0014525 0.0001689 619.7714 -8.6006535 0.0000000 6
Eagle SUPER AFR - EAS 0 -0.0042507 0.0002094 619.7714 -20.3026035 0.0000000 6
Eagle SUPER AFR - EUR 0 -0.0010349 0.0001824 619.7714 -5.6728974 0.0000002 6
Eagle SUPER AFR - SAS 0 -0.0032724 0.0001972 619.7714 -16.5921877 0.0000000 6
Eagle SUPER AMR - EAS 0 -0.0027982 0.0002219 619.7714 -12.6106311 0.0000000 6
Eagle SUPER AMR - EUR 0 0.0004177 0.0001967 619.7714 2.1236894 0.2112593 6
Eagle SUPER AMR - SAS 0 -0.0018199 0.0002105 619.7714 -8.6467229 0.0000000 6
Eagle SUPER EAS - EUR 0 0.0032158 0.0002324 619.7714 13.8399410 0.0000000 6
Eagle SUPER EAS - SAS 0 0.0009783 0.0002442 619.7714 4.0067414 0.0006578 6
Eagle SUPER EUR - SAS 0 -0.0022376 0.0002215 619.7714 -10.1026708 0.0000000 6
SHAPEIT SUPER AFR - AMR 0 -0.0011273 0.0001689 619.7714 -6.6748165 0.0000000 6
SHAPEIT SUPER AFR - EAS 0 -0.0037636 0.0002094 619.7714 -17.9762149 0.0000000 6
SHAPEIT SUPER AFR - EUR 0 -0.0005196 0.0001824 619.7714 -2.8482309 0.0365645 6
SHAPEIT SUPER AFR - SAS 0 -0.0031023 0.0001972 619.7714 -15.7294721 0.0000000 6
SHAPEIT SUPER AMR - EAS 0 -0.0026363 0.0002219 619.7714 -11.8813333 0.0000000 6
SHAPEIT SUPER AMR - EUR 0 0.0006077 0.0001967 619.7714 3.0899647 0.0177762 6
SHAPEIT SUPER AMR - SAS 0 -0.0019750 0.0002105 619.7714 -9.3836041 0.0000000 6
SHAPEIT SUPER EAS - EUR 0 0.0032440 0.0002324 619.7714 13.9613549 0.0000000 6
SHAPEIT SUPER EAS - SAS 0 0.0006613 0.0002442 619.7714 2.7087206 0.0538020 6
SHAPEIT SUPER EUR - SAS 0 -0.0025827 0.0002215 619.7714 -11.6609377 0.0000000 6
Beagle SUPER AFR - AMR 0 -0.0011244 0.0001844 622.9174 -6.0965236 0.0000000 7
Beagle SUPER AFR - EAS 0 -0.0042376 0.0002286 622.9174 -18.5336840 0.0000000 7
Beagle SUPER AFR - EUR 0 -0.0006582 0.0001992 622.9174 -3.3037046 0.0089057 7
Beagle SUPER AFR - SAS 0 -0.0032267 0.0002154 622.9174 -14.9807430 0.0000000 7
Beagle SUPER AMR - EAS 0 -0.0031132 0.0002423 622.9174 -12.8474905 0.0000000 7
Beagle SUPER AMR - EUR 0 0.0004663 0.0002148 622.9174 2.1708866 0.1921619 7
Beagle SUPER AMR - SAS 0 -0.0021022 0.0002299 622.9174 -9.1460225 0.0000000 7
Beagle SUPER EAS - EUR 0 0.0035795 0.0002538 622.9174 14.1060761 0.0000000 7
Beagle SUPER EAS - SAS 0 0.0010110 0.0002666 622.9174 3.7915799 0.0015384 7
Beagle SUPER EUR - SAS 0 -0.0025685 0.0002419 622.9174 -10.6190609 0.0000000 7
Eagle SUPER AFR - AMR 0 -0.0014571 0.0001844 622.9174 -7.9002640 0.0000000 7
Eagle SUPER AFR - EAS 0 -0.0047337 0.0002286 622.9174 -20.7034351 0.0000000 7
Eagle SUPER AFR - EUR 0 -0.0011198 0.0001992 622.9174 -5.6209473 0.0000003 7
Eagle SUPER AFR - SAS 0 -0.0035554 0.0002154 622.9174 -16.5069426 0.0000000 7
Eagle SUPER AMR - EAS 0 -0.0032766 0.0002423 622.9174 -13.5219213 0.0000000 7
Eagle SUPER AMR - EUR 0 0.0003373 0.0002148 622.9174 1.5704299 0.5170067 7
Eagle SUPER AMR - SAS 0 -0.0020983 0.0002299 622.9174 -9.1288384 0.0000000 7
Eagle SUPER EAS - EUR 0 0.0036139 0.0002538 622.9174 14.2418953 0.0000000 7
Eagle SUPER EAS - SAS 0 0.0011784 0.0002666 622.9174 4.4193220 0.0001137 7
Eagle SUPER EUR - SAS 0 -0.0024356 0.0002419 622.9174 -10.0695494 0.0000000 7
SHAPEIT SUPER AFR - AMR 0 -0.0011969 0.0001844 622.9174 -6.4894864 0.0000000 7
SHAPEIT SUPER AFR - EAS 0 -0.0043577 0.0002286 622.9174 -19.0587872 0.0000000 7
SHAPEIT SUPER AFR - EUR 0 -0.0005605 0.0001992 622.9174 -2.8134642 0.0403378 7
SHAPEIT SUPER AFR - SAS 0 -0.0034356 0.0002154 622.9174 -15.9507131 0.0000000 7
SHAPEIT SUPER AMR - EAS 0 -0.0031608 0.0002423 622.9174 -13.0438658 0.0000000 7
SHAPEIT SUPER AMR - EUR 0 0.0006364 0.0002148 622.9174 2.9630642 0.0261650 7
SHAPEIT SUPER AMR - SAS 0 -0.0022387 0.0002299 622.9174 -9.7396305 0.0000000 7
SHAPEIT SUPER EAS - EUR 0 0.0037972 0.0002538 622.9174 14.9641009 0.0000000 7
SHAPEIT SUPER EAS - SAS 0 0.0009221 0.0002666 622.9174 3.4583276 0.0052416 7
SHAPEIT SUPER EUR - SAS 0 -0.0028751 0.0002419 622.9174 -11.8865845 0.0000000 7
Beagle SUPER AFR - AMR 0 -0.0014515 0.0001926 630.1012 -7.5359547 0.0000000 8
Beagle SUPER AFR - EAS 0 -0.0046079 0.0002388 630.1012 -19.2983258 0.0000000 8
Beagle SUPER AFR - EUR 0 -0.0009419 0.0002080 630.1012 -4.5272532 0.0000699 8
Beagle SUPER AFR - SAS 0 -0.0033096 0.0002249 630.1012 -14.7139826 0.0000000 8
Beagle SUPER AMR - EAS 0 -0.0031564 0.0002531 630.1012 -12.4733969 0.0000000 8
Beagle SUPER AMR - EUR 0 0.0005096 0.0002243 630.1012 2.2720546 0.1553620 8
Beagle SUPER AMR - SAS 0 -0.0018581 0.0002400 630.1012 -7.7410453 0.0000000 8
Beagle SUPER EAS - EUR 0 0.0036660 0.0002650 630.1012 13.8344658 0.0000000 8
Beagle SUPER EAS - SAS 0 0.0012983 0.0002784 630.1012 4.6627614 0.0000374 8
Beagle SUPER EUR - SAS 0 -0.0023677 0.0002526 630.1012 -9.3737543 0.0000000 8
Eagle SUPER AFR - AMR 0 -0.0020009 0.0001926 630.1012 -10.3885469 0.0000000 8
Eagle SUPER AFR - EAS 0 -0.0052729 0.0002388 630.1012 -22.0836020 0.0000000 8
Eagle SUPER AFR - EUR 0 -0.0015167 0.0002080 630.1012 -7.2904244 0.0000000 8
Eagle SUPER AFR - SAS 0 -0.0037314 0.0002249 630.1012 -16.5895812 0.0000000 8
Eagle SUPER AMR - EAS 0 -0.0032721 0.0002531 630.1012 -12.9303112 0.0000000 8
Eagle SUPER AMR - EUR 0 0.0004842 0.0002243 630.1012 2.1586537 0.1969751 8
Eagle SUPER AMR - SAS 0 -0.0017306 0.0002400 630.1012 -7.2096669 0.0000000 8
Eagle SUPER EAS - EUR 0 0.0037562 0.0002650 630.1012 14.1748115 0.0000000 8
Eagle SUPER EAS - SAS 0 0.0015415 0.0002784 630.1012 5.5360841 0.0000005 8
Eagle SUPER EUR - SAS 0 -0.0022147 0.0002526 630.1012 -8.7680936 0.0000000 8
SHAPEIT SUPER AFR - AMR 0 -0.0016379 0.0001926 630.1012 -8.5037740 0.0000000 8
SHAPEIT SUPER AFR - EAS 0 -0.0046015 0.0002388 630.1012 -19.2714578 0.0000000 8
SHAPEIT SUPER AFR - EUR 0 -0.0008229 0.0002080 630.1012 -3.9554378 0.0008075 8
SHAPEIT SUPER AFR - SAS 0 -0.0034985 0.0002249 630.1012 -15.5540680 0.0000000 8
SHAPEIT SUPER AMR - EAS 0 -0.0029636 0.0002531 630.1012 -11.7114181 0.0000000 8
SHAPEIT SUPER AMR - EUR 0 0.0008150 0.0002243 630.1012 3.6335453 0.0027878 8
SHAPEIT SUPER AMR - SAS 0 -0.0018607 0.0002400 630.1012 -7.7516758 0.0000000 8
SHAPEIT SUPER EAS - EUR 0 0.0037786 0.0002650 630.1012 14.2591805 0.0000000 8
SHAPEIT SUPER EAS - SAS 0 0.0011029 0.0002784 630.1012 3.9611044 0.0007894 8
SHAPEIT SUPER EUR - SAS 0 -0.0026756 0.0002526 630.1012 -10.5928058 0.0000000 8
Beagle SUPER AFR - AMR 0 -0.0009670 0.0002020 622.7189 -4.7865984 0.0000209 9
Beagle SUPER AFR - EAS 0 -0.0046635 0.0002504 622.7189 -18.6211034 0.0000000 9
Beagle SUPER AFR - EUR 0 -0.0009076 0.0002182 622.7189 -4.1592306 0.0003503 9
Beagle SUPER AFR - SAS 0 -0.0034326 0.0002359 622.7189 -14.5497417 0.0000000 9
Beagle SUPER AMR - EAS 0 -0.0036965 0.0002654 622.7189 -13.9269870 0.0000000 9
Beagle SUPER AMR - EUR 0 0.0000594 0.0002353 622.7189 0.2524599 0.9991039 9
Beagle SUPER AMR - SAS 0 -0.0024656 0.0002518 622.7189 -9.7932369 0.0000000 9
Beagle SUPER EAS - EUR 0 0.0037559 0.0002779 622.7189 13.5131842 0.0000000 9
Beagle SUPER EAS - SAS 0 0.0012309 0.0002921 622.7189 4.2147044 0.0002770 9
Beagle SUPER EUR - SAS 0 -0.0025250 0.0002649 622.7189 -9.5306177 0.0000000 9
Eagle SUPER AFR - AMR 0 -0.0014238 0.0002020 622.7189 -7.0478436 0.0000000 9
Eagle SUPER AFR - EAS 0 -0.0054288 0.0002504 622.7189 -21.6771002 0.0000000 9
Eagle SUPER AFR - EUR 0 -0.0014196 0.0002182 622.7189 -6.5055944 0.0000000 9
Eagle SUPER AFR - SAS 0 -0.0037863 0.0002359 622.7189 -16.0492072 0.0000000 9
Eagle SUPER AMR - EAS 0 -0.0040050 0.0002654 622.7189 -15.0894294 0.0000000 9
Eagle SUPER AMR - EUR 0 0.0000042 0.0002353 622.7189 0.0178652 1.0000000 9
Eagle SUPER AMR - SAS 0 -0.0023625 0.0002518 622.7189 -9.3838974 0.0000000 9
Eagle SUPER EAS - EUR 0 0.0040092 0.0002779 622.7189 14.4246920 0.0000000 9
Eagle SUPER EAS - SAS 0 0.0016425 0.0002921 622.7189 5.6240134 0.0000003 9
Eagle SUPER EUR - SAS 0 -0.0023667 0.0002649 622.7189 -8.9333145 0.0000000 9
SHAPEIT SUPER AFR - AMR 0 -0.0011353 0.0002020 622.7189 -5.6198815 0.0000003 9
SHAPEIT SUPER AFR - EAS 0 -0.0048050 0.0002504 622.7189 -19.1862858 0.0000000 9
SHAPEIT SUPER AFR - EUR 0 -0.0007718 0.0002182 622.7189 -3.5367896 0.0039676 9
SHAPEIT SUPER AFR - SAS 0 -0.0036449 0.0002359 622.7189 -15.4496997 0.0000000 9
SHAPEIT SUPER AMR - EAS 0 -0.0036697 0.0002654 622.7189 -13.8260429 0.0000000 9
SHAPEIT SUPER AMR - EUR 0 0.0003636 0.0002353 622.7189 1.5453785 0.5332710 9
SHAPEIT SUPER AMR - SAS 0 -0.0025096 0.0002518 622.7189 -9.9679242 0.0000000 9
SHAPEIT SUPER EAS - EUR 0 0.0040333 0.0002779 622.7189 14.5111111 0.0000000 9
SHAPEIT SUPER EAS - SAS 0 0.0011601 0.0002921 622.7189 3.9723762 0.0007553 9
SHAPEIT SUPER EUR - SAS 0 -0.0028731 0.0002649 622.7189 -10.8446819 0.0000000 9
Beagle SUPER AFR - AMR 0 -0.0010874 0.0001749 626.1417 -6.2164281 0.0000000 10
Beagle SUPER AFR - EAS 0 -0.0039478 0.0002168 626.1417 -18.2054827 0.0000000 10
Beagle SUPER AFR - EUR 0 -0.0006912 0.0001889 626.1417 -3.6581915 0.0025459 10
Beagle SUPER AFR - SAS 0 -0.0031931 0.0002043 626.1417 -15.6313950 0.0000000 10
Beagle SUPER AMR - EAS 0 -0.0028604 0.0002298 626.1417 -12.4465504 0.0000000 10
Beagle SUPER AMR - EUR 0 0.0003962 0.0002037 626.1417 1.9450439 0.2946378 10
Beagle SUPER AMR - SAS 0 -0.0021057 0.0002180 626.1417 -9.6595124 0.0000000 10
Beagle SUPER EAS - EUR 0 0.0032566 0.0002407 626.1417 13.5320479 0.0000000 10
Beagle SUPER EAS - SAS 0 0.0007547 0.0002529 626.1417 2.9845479 0.0245333 10
Beagle SUPER EUR - SAS 0 -0.0025019 0.0002294 626.1417 -10.9064875 0.0000000 10
Eagle SUPER AFR - AMR 0 -0.0015247 0.0001749 626.1417 -8.7164454 0.0000000 10
Eagle SUPER AFR - EAS 0 -0.0046306 0.0002168 626.1417 -21.3542536 0.0000000 10
Eagle SUPER AFR - EUR 0 -0.0011621 0.0001889 626.1417 -6.1505598 0.0000000 10
Eagle SUPER AFR - SAS 0 -0.0036710 0.0002043 626.1417 -17.9710118 0.0000000 10
Eagle SUPER AMR - EAS 0 -0.0031059 0.0002298 626.1417 -13.5147965 0.0000000 10
Eagle SUPER AMR - EUR 0 0.0003626 0.0002037 626.1417 1.7800623 0.3861436 10
Eagle SUPER AMR - SAS 0 -0.0021463 0.0002180 626.1417 -9.8458560 0.0000000 10
Eagle SUPER EAS - EUR 0 0.0034685 0.0002407 626.1417 14.4125238 0.0000000 10
Eagle SUPER EAS - SAS 0 0.0009596 0.0002529 626.1417 3.7947418 0.0015191 10
Eagle SUPER EUR - SAS 0 -0.0025089 0.0002294 626.1417 -10.9370712 0.0000000 10
SHAPEIT SUPER AFR - AMR 0 -0.0012013 0.0001749 626.1417 -6.8678015 0.0000000 10
SHAPEIT SUPER AFR - EAS 0 -0.0041689 0.0002168 626.1417 -19.2250673 0.0000000 10
SHAPEIT SUPER AFR - EUR 0 -0.0005814 0.0001889 626.1417 -3.0773001 0.0184835 10
SHAPEIT SUPER AFR - SAS 0 -0.0034282 0.0002043 626.1417 -16.7823108 0.0000000 10
SHAPEIT SUPER AMR - EAS 0 -0.0029676 0.0002298 626.1417 -12.9128181 0.0000000 10
SHAPEIT SUPER AMR - EUR 0 0.0006199 0.0002037 626.1417 3.0432112 0.0205333 10
SHAPEIT SUPER AMR - SAS 0 -0.0022269 0.0002180 626.1417 -10.2153282 0.0000000 10
SHAPEIT SUPER EAS - EUR 0 0.0035875 0.0002407 626.1417 14.9067938 0.0000000 10
SHAPEIT SUPER EAS - SAS 0 0.0007407 0.0002529 626.1417 2.9291549 0.0289217 10
SHAPEIT SUPER EUR - SAS 0 -0.0028467 0.0002294 626.1417 -12.4098040 0.0000000 10
Beagle SUPER AFR - AMR 0 -0.0014214 0.0001955 623.5183 -7.2691170 0.0000000 11
Beagle SUPER AFR - EAS 0 -0.0043086 0.0002424 623.5183 -17.7742435 0.0000000 11
Beagle SUPER AFR - EUR 0 -0.0008648 0.0002112 623.5183 -4.0946807 0.0004584 11
Beagle SUPER AFR - SAS 0 -0.0036206 0.0002284 623.5183 -15.8554625 0.0000000 11
Beagle SUPER AMR - EAS 0 -0.0028872 0.0002569 623.5183 -11.2384264 0.0000000 11
Beagle SUPER AMR - EUR 0 0.0005565 0.0002277 623.5183 2.4441503 0.1051370 11
Beagle SUPER AMR - SAS 0 -0.0021992 0.0002437 623.5183 -9.0247957 0.0000000 11
Beagle SUPER EAS - EUR 0 0.0034438 0.0002690 623.5183 12.8007987 0.0000000 11
Beagle SUPER EAS - SAS 0 0.0006880 0.0002827 623.5183 2.4337520 0.1077584 11
Beagle SUPER EUR - SAS 0 -0.0027558 0.0002564 623.5183 -10.7465072 0.0000000 11
Eagle SUPER AFR - AMR 0 -0.0018680 0.0001955 623.5183 -9.5529109 0.0000000 11
Eagle SUPER AFR - EAS 0 -0.0049399 0.0002424 623.5183 -20.3782727 0.0000000 11
Eagle SUPER AFR - EUR 0 -0.0014279 0.0002112 623.5183 -6.7606011 0.0000000 11
Eagle SUPER AFR - SAS 0 -0.0040539 0.0002284 623.5183 -17.7526824 0.0000000 11
Eagle SUPER AMR - EAS 0 -0.0030719 0.0002569 623.5183 -11.9572470 0.0000000 11
Eagle SUPER AMR - EUR 0 0.0004400 0.0002277 623.5183 1.9325106 0.3011351 11
Eagle SUPER AMR - SAS 0 -0.0021859 0.0002437 623.5183 -8.9700839 0.0000000 11
Eagle SUPER EAS - EUR 0 0.0035119 0.0002690 623.5183 13.0541821 0.0000000 11
Eagle SUPER EAS - SAS 0 0.0008860 0.0002827 623.5183 3.1341868 0.0154671 11
Eagle SUPER EUR - SAS 0 -0.0026260 0.0002564 623.5183 -10.2401994 0.0000000 11
SHAPEIT SUPER AFR - AMR 0 -0.0015101 0.0001955 623.5183 -7.7227364 0.0000000 11
SHAPEIT SUPER AFR - EAS 0 -0.0044835 0.0002424 623.5183 -18.4954733 0.0000000 11
SHAPEIT SUPER AFR - EUR 0 -0.0007548 0.0002112 623.5183 -3.5735260 0.0034748 11
SHAPEIT SUPER AFR - SAS 0 -0.0037782 0.0002284 623.5183 -16.5455945 0.0000000 11
SHAPEIT SUPER AMR - EAS 0 -0.0029734 0.0002569 623.5183 -11.5736924 0.0000000 11
SHAPEIT SUPER AMR - EUR 0 0.0007553 0.0002277 623.5183 3.3170905 0.0085143 11
SHAPEIT SUPER AMR - SAS 0 -0.0022681 0.0002437 623.5183 -9.3075066 0.0000000 11
SHAPEIT SUPER EAS - EUR 0 0.0037287 0.0002690 623.5183 13.8598135 0.0000000 11
SHAPEIT SUPER EAS - SAS 0 0.0007052 0.0002827 623.5183 2.4947337 0.0930927 11
SHAPEIT SUPER EUR - SAS 0 -0.0030235 0.0002564 623.5183 -11.7903015 0.0000000 11
Beagle SUPER AFR - AMR 0 -0.0012389 0.0002167 630.4754 -5.7179370 0.0000002 12
Beagle SUPER AFR - EAS 0 -0.0043150 0.0002686 630.4754 -16.0637948 0.0000000 12
Beagle SUPER AFR - EUR 0 -0.0008773 0.0002340 630.4754 -3.7484051 0.0018128 12
Beagle SUPER AFR - SAS 0 -0.0037226 0.0002530 630.4754 -14.7116726 0.0000000 12
Beagle SUPER AMR - EAS 0 -0.0030760 0.0002847 630.4754 -10.8051470 0.0000000 12
Beagle SUPER AMR - EUR 0 0.0003617 0.0002523 630.4754 1.4332954 0.6063265 12
Beagle SUPER AMR - SAS 0 -0.0024837 0.0002700 630.4754 -9.1976661 0.0000000 12
Beagle SUPER EAS - EUR 0 0.0034377 0.0002981 630.4754 11.5314557 0.0000000 12
Beagle SUPER EAS - SAS 0 0.0005923 0.0003132 630.4754 1.8909609 0.3232130 12
Beagle SUPER EUR - SAS 0 -0.0028453 0.0002842 630.4754 -10.0131858 0.0000000 12
Eagle SUPER AFR - AMR 0 -0.0017589 0.0002167 630.4754 -8.1177207 0.0000000 12
Eagle SUPER AFR - EAS 0 -0.0050468 0.0002686 630.4754 -18.7882745 0.0000000 12
Eagle SUPER AFR - EUR 0 -0.0014243 0.0002340 630.4754 -6.0857113 0.0000000 12
Eagle SUPER AFR - SAS 0 -0.0039907 0.0002530 630.4754 -15.7709406 0.0000000 12
Eagle SUPER AMR - EAS 0 -0.0032879 0.0002847 630.4754 -11.5493379 0.0000000 12
Eagle SUPER AMR - EUR 0 0.0003346 0.0002523 630.4754 1.3260696 0.6750394 12
Eagle SUPER AMR - SAS 0 -0.0022318 0.0002700 630.4754 -8.2646700 0.0000000 12
Eagle SUPER EAS - EUR 0 0.0036225 0.0002981 630.4754 12.1513612 0.0000000 12
Eagle SUPER EAS - SAS 0 0.0010561 0.0003132 630.4754 3.3715777 0.0070742 12
Eagle SUPER EUR - SAS 0 -0.0025664 0.0002842 630.4754 -9.0313541 0.0000000 12
SHAPEIT SUPER AFR - AMR 0 -0.0014038 0.0002167 630.4754 -6.4789055 0.0000000 12
SHAPEIT SUPER AFR - EAS 0 -0.0045536 0.0002686 630.4754 -16.9521030 0.0000000 12
SHAPEIT SUPER AFR - EUR 0 -0.0008387 0.0002340 630.4754 -3.5832924 0.0033511 12
SHAPEIT SUPER AFR - SAS 0 -0.0040962 0.0002530 630.4754 -16.1878915 0.0000000 12
SHAPEIT SUPER AMR - EAS 0 -0.0031498 0.0002847 630.4754 -11.0641321 0.0000000 12
SHAPEIT SUPER AMR - EUR 0 0.0005652 0.0002523 630.4754 2.2399150 0.1664425 12
SHAPEIT SUPER AMR - SAS 0 -0.0026924 0.0002700 630.4754 -9.9703718 0.0000000 12
SHAPEIT SUPER EAS - EUR 0 0.0037149 0.0002981 630.4754 12.4614929 0.0000000 12
SHAPEIT SUPER EAS - SAS 0 0.0004574 0.0003132 630.4754 1.4602176 0.5888040 12
SHAPEIT SUPER EUR - SAS 0 -0.0032575 0.0002842 630.4754 -11.4637287 0.0000000 12
Beagle SUPER AFR - AMR 0 -0.0010116 0.0001894 639.1797 -5.3420672 0.0000013 13
Beagle SUPER AFR - EAS 0 -0.0041622 0.0002348 639.1797 -17.7301525 0.0000000 13
Beagle SUPER AFR - EUR 0 -0.0008443 0.0002045 639.1797 -4.1278110 0.0003983 13
Beagle SUPER AFR - SAS 0 -0.0031188 0.0002211 639.1797 -14.1030464 0.0000000 13
Beagle SUPER AMR - EAS 0 -0.0031506 0.0002488 639.1797 -12.6635410 0.0000000 13
Beagle SUPER AMR - EUR 0 0.0001673 0.0002205 639.1797 0.7586019 0.9422196 13
Beagle SUPER AMR - SAS 0 -0.0021072 0.0002360 639.1797 -8.9289446 0.0000000 13
Beagle SUPER EAS - EUR 0 0.0033179 0.0002605 639.1797 12.7350603 0.0000000 13
Beagle SUPER EAS - SAS 0 0.0010434 0.0002738 639.1797 3.8115371 0.0014213 13
Beagle SUPER EUR - SAS 0 -0.0022745 0.0002483 639.1797 -9.1587208 0.0000000 13
Eagle SUPER AFR - AMR 0 -0.0014869 0.0001894 639.1797 -7.8521398 0.0000000 13
Eagle SUPER AFR - EAS 0 -0.0049285 0.0002348 639.1797 -20.9943993 0.0000000 13
Eagle SUPER AFR - EUR 0 -0.0013932 0.0002045 639.1797 -6.8115103 0.0000000 13
Eagle SUPER AFR - SAS 0 -0.0038451 0.0002211 639.1797 -17.3873847 0.0000000 13
Eagle SUPER AMR - EAS 0 -0.0034416 0.0002488 639.1797 -13.8330924 0.0000000 13
Eagle SUPER AMR - EUR 0 0.0000937 0.0002205 639.1797 0.4247838 0.9931976 13
Eagle SUPER AMR - SAS 0 -0.0023582 0.0002360 639.1797 -9.9924832 0.0000000 13
Eagle SUPER EAS - EUR 0 0.0035353 0.0002605 639.1797 13.5693745 0.0000000 13
Eagle SUPER EAS - SAS 0 0.0010834 0.0002738 639.1797 3.9576118 0.0007994 13
Eagle SUPER EUR - SAS 0 -0.0024518 0.0002483 639.1797 -9.8729767 0.0000000 13
SHAPEIT SUPER AFR - AMR 0 -0.0011737 0.0001894 639.1797 -6.1981607 0.0000000 13
SHAPEIT SUPER AFR - EAS 0 -0.0042709 0.0002348 639.1797 -18.1933113 0.0000000 13
SHAPEIT SUPER AFR - EUR 0 -0.0007486 0.0002045 639.1797 -3.6598952 0.0025260 13
SHAPEIT SUPER AFR - SAS 0 -0.0034515 0.0002211 639.1797 -15.6076484 0.0000000 13
SHAPEIT SUPER AMR - EAS 0 -0.0030972 0.0002488 639.1797 -12.4489696 0.0000000 13
SHAPEIT SUPER AMR - EUR 0 0.0004251 0.0002205 639.1797 1.9277768 0.3035797 13
SHAPEIT SUPER AMR - SAS 0 -0.0022778 0.0002360 639.1797 -9.6519183 0.0000000 13
SHAPEIT SUPER EAS - EUR 0 0.0035223 0.0002605 639.1797 13.5197433 0.0000000 13
SHAPEIT SUPER EAS - SAS 0 0.0008194 0.0002738 639.1797 2.9932930 0.0238810 13
SHAPEIT SUPER EUR - SAS 0 -0.0027029 0.0002483 639.1797 -10.8839383 0.0000000 13
Beagle SUPER AFR - AMR 0 -0.0014573 0.0002031 629.1835 -7.1750953 0.0000000 14
Beagle SUPER AFR - EAS 0 -0.0041591 0.0002518 629.1835 -16.5181164 0.0000000 14
Beagle SUPER AFR - EUR 0 -0.0007848 0.0002194 629.1835 -3.5770367 0.0034287 14
Beagle SUPER AFR - SAS 0 -0.0034408 0.0002372 629.1835 -14.5066154 0.0000000 14
Beagle SUPER AMR - EAS 0 -0.0027018 0.0002669 629.1835 -10.1247544 0.0000000 14
Beagle SUPER AMR - EUR 0 0.0006726 0.0002365 629.1835 2.8435576 0.0370395 14
Beagle SUPER AMR - SAS 0 -0.0019835 0.0002531 629.1835 -7.8362844 0.0000000 14
Beagle SUPER EAS - EUR 0 0.0033744 0.0002794 629.1835 12.0753608 0.0000000 14
Beagle SUPER EAS - SAS 0 0.0007183 0.0002936 629.1835 2.4461938 0.1046155 14
Beagle SUPER EUR - SAS 0 -0.0026561 0.0002664 629.1835 -9.9717311 0.0000000 14
Eagle SUPER AFR - AMR 0 -0.0019261 0.0002031 629.1835 -9.4832583 0.0000000 14
Eagle SUPER AFR - EAS 0 -0.0050255 0.0002518 629.1835 -19.9590968 0.0000000 14
Eagle SUPER AFR - EUR 0 -0.0013647 0.0002194 629.1835 -6.2207193 0.0000000 14
Eagle SUPER AFR - SAS 0 -0.0038465 0.0002372 629.1835 -16.2166672 0.0000000 14
Eagle SUPER AMR - EAS 0 -0.0030994 0.0002669 629.1835 -11.6147426 0.0000000 14
Eagle SUPER AMR - EUR 0 0.0005614 0.0002365 629.1835 2.3734712 0.1239617 14
Eagle SUPER AMR - SAS 0 -0.0019203 0.0002531 629.1835 -7.5866305 0.0000000 14
Eagle SUPER EAS - EUR 0 0.0036608 0.0002794 629.1835 13.1003372 0.0000000 14
Eagle SUPER EAS - SAS 0 0.0011791 0.0002936 629.1835 4.0155222 0.0006337 14
Eagle SUPER EUR - SAS 0 -0.0024817 0.0002664 629.1835 -9.3170689 0.0000000 14
SHAPEIT SUPER AFR - AMR 0 -0.0016062 0.0002031 629.1835 -7.9083633 0.0000000 14
SHAPEIT SUPER AFR - EAS 0 -0.0044053 0.0002518 629.1835 -17.4959964 0.0000000 14
SHAPEIT SUPER AFR - EUR 0 -0.0007646 0.0002194 629.1835 -3.4850092 0.0047685 14
SHAPEIT SUPER AFR - SAS 0 -0.0036953 0.0002372 629.1835 -15.5792335 0.0000000 14
SHAPEIT SUPER AMR - EAS 0 -0.0027991 0.0002669 629.1835 -10.4893395 0.0000000 14
SHAPEIT SUPER AMR - EUR 0 0.0008417 0.0002365 629.1835 3.5585990 0.0036655 14
SHAPEIT SUPER AMR - SAS 0 -0.0020890 0.0002531 629.1835 -8.2530176 0.0000000 14
SHAPEIT SUPER EAS - EUR 0 0.0036408 0.0002794 629.1835 13.0287286 0.0000000 14
SHAPEIT SUPER EAS - SAS 0 0.0007101 0.0002936 629.1835 2.4182868 0.1117392 14
SHAPEIT SUPER EUR - SAS 0 -0.0029307 0.0002664 629.1835 -11.0026781 0.0000000 14
Beagle SUPER AFR - AMR 0 -0.0010614 0.0002245 625.9843 -4.7276363 0.0000276 15
Beagle SUPER AFR - EAS 0 -0.0047660 0.0002783 625.9843 -17.1244395 0.0000000 15
Beagle SUPER AFR - EUR 0 -0.0011094 0.0002425 625.9843 -4.5747598 0.0000563 15
Beagle SUPER AFR - SAS 0 -0.0036459 0.0002622 625.9843 -13.9065239 0.0000000 15
Beagle SUPER AMR - EAS 0 -0.0037046 0.0002950 625.9843 -12.5596691 0.0000000 15
Beagle SUPER AMR - EUR 0 -0.0000480 0.0002614 625.9843 -0.1836016 0.9997458 15
Beagle SUPER AMR - SAS 0 -0.0025846 0.0002798 625.9843 -9.2378127 0.0000000 15
Beagle SUPER EAS - EUR 0 0.0036566 0.0003089 625.9843 11.8383898 0.0000000 15
Beagle SUPER EAS - SAS 0 0.0011200 0.0003246 625.9843 3.4508776 0.0053787 15
Beagle SUPER EUR - SAS 0 -0.0025366 0.0002944 625.9843 -8.6155968 0.0000000 15
Eagle SUPER AFR - AMR 0 -0.0014429 0.0002245 625.9843 -6.4272183 0.0000000 15
Eagle SUPER AFR - EAS 0 -0.0053909 0.0002783 625.9843 -19.3698530 0.0000000 15
Eagle SUPER AFR - EUR 0 -0.0015275 0.0002425 625.9843 -6.2991073 0.0000000 15
Eagle SUPER AFR - SAS 0 -0.0041471 0.0002622 625.9843 -15.8180651 0.0000000 15
Eagle SUPER AMR - EAS 0 -0.0039480 0.0002950 625.9843 -13.3847692 0.0000000 15
Eagle SUPER AMR - EUR 0 -0.0000846 0.0002614 625.9843 -0.3235557 0.9976281 15
Eagle SUPER AMR - SAS 0 -0.0027042 0.0002798 625.9843 -9.6652951 0.0000000 15
Eagle SUPER EAS - EUR 0 0.0038634 0.0003089 625.9843 12.5078580 0.0000000 15
Eagle SUPER EAS - SAS 0 0.0012438 0.0003246 625.9843 3.8322244 0.0013141 15
Eagle SUPER EUR - SAS 0 -0.0026196 0.0002944 625.9843 -8.8975567 0.0000000 15
SHAPEIT SUPER AFR - AMR 0 -0.0012750 0.0002245 625.9843 -5.6793027 0.0000002 15
SHAPEIT SUPER AFR - EAS 0 -0.0050149 0.0002783 625.9843 -18.0189972 0.0000000 15
SHAPEIT SUPER AFR - EUR 0 -0.0010286 0.0002425 625.9843 -4.2419313 0.0002465 15
SHAPEIT SUPER AFR - SAS 0 -0.0040806 0.0002622 625.9843 -15.5645729 0.0000000 15
SHAPEIT SUPER AMR - EAS 0 -0.0037399 0.0002950 625.9843 -12.6794070 0.0000000 15
SHAPEIT SUPER AMR - EUR 0 0.0002464 0.0002614 625.9843 0.9423430 0.8802320 15
SHAPEIT SUPER AMR - SAS 0 -0.0028056 0.0002798 625.9843 -10.0278877 0.0000000 15
SHAPEIT SUPER EAS - EUR 0 0.0039863 0.0003089 625.9843 12.9057295 0.0000000 15
SHAPEIT SUPER EAS - SAS 0 0.0009343 0.0003246 625.9843 2.8786119 0.0335069 15
SHAPEIT SUPER EUR - SAS 0 -0.0030520 0.0002944 625.9843 -10.3661934 0.0000000 15
Beagle SUPER AFR - AMR 0 -0.0014752 0.0002468 635.1038 -5.9760746 0.0000000 16
Beagle SUPER AFR - EAS 0 -0.0052671 0.0003060 635.1038 -17.2117779 0.0000000 16
Beagle SUPER AFR - EUR 0 -0.0008846 0.0002666 635.1038 -3.3177969 0.0084863 16
Beagle SUPER AFR - SAS 0 -0.0040924 0.0002883 635.1038 -14.1961532 0.0000000 16
Beagle SUPER AMR - EAS 0 -0.0037919 0.0003243 635.1038 -11.6918664 0.0000000 16
Beagle SUPER AMR - EUR 0 0.0005905 0.0002875 635.1038 2.0543818 0.2415070 16
Beagle SUPER AMR - SAS 0 -0.0026172 0.0003076 635.1038 -8.5074612 0.0000000 16
Beagle SUPER EAS - EUR 0 0.0043825 0.0003396 635.1038 12.9039097 0.0000000 16
Beagle SUPER EAS - SAS 0 0.0011747 0.0003569 635.1038 3.2918106 0.0092581 16
Beagle SUPER EUR - SAS 0 -0.0032078 0.0003237 635.1038 -9.9087891 0.0000000 16
Eagle SUPER AFR - AMR 0 -0.0017876 0.0002468 635.1038 -7.2415754 0.0000000 16
Eagle SUPER AFR - EAS 0 -0.0058365 0.0003060 635.1038 -19.0723537 0.0000000 16
Eagle SUPER AFR - EUR 0 -0.0015439 0.0002666 635.1038 -5.7903934 0.0000001 16
Eagle SUPER AFR - SAS 0 -0.0040591 0.0002883 635.1038 -14.0806415 0.0000000 16
Eagle SUPER AMR - EAS 0 -0.0040489 0.0003243 635.1038 -12.4842363 0.0000000 16
Eagle SUPER AMR - EUR 0 0.0002437 0.0002875 635.1038 0.8476218 0.9155117 16
Eagle SUPER AMR - SAS 0 -0.0022715 0.0003076 635.1038 -7.3837761 0.0000000 16
Eagle SUPER EAS - EUR 0 0.0042926 0.0003396 635.1038 12.6391805 0.0000000 16
Eagle SUPER EAS - SAS 0 0.0017774 0.0003569 635.1038 4.9805965 0.0000081 16
Eagle SUPER EUR - SAS 0 -0.0025152 0.0003237 635.1038 -7.7694042 0.0000000 16
SHAPEIT SUPER AFR - AMR 0 -0.0017040 0.0002468 635.1038 -6.9028705 0.0000000 16
SHAPEIT SUPER AFR - EAS 0 -0.0054842 0.0003060 635.1038 -17.9211335 0.0000000 16
SHAPEIT SUPER AFR - EUR 0 -0.0010933 0.0002666 635.1038 -4.1003796 0.0004468 16
SHAPEIT SUPER AFR - SAS 0 -0.0042918 0.0002883 635.1038 -14.8879181 0.0000000 16
SHAPEIT SUPER AMR - EAS 0 -0.0037802 0.0003243 635.1038 -11.6557840 0.0000000 16
SHAPEIT SUPER AMR - EUR 0 0.0006107 0.0002875 635.1038 2.1243569 0.2109475 16
SHAPEIT SUPER AMR - SAS 0 -0.0025878 0.0003076 635.1038 -8.4120234 0.0000000 16
SHAPEIT SUPER EAS - EUR 0 0.0043909 0.0003396 635.1038 12.9286797 0.0000000 16
SHAPEIT SUPER EAS - SAS 0 0.0011924 0.0003569 635.1038 3.3412908 0.0078393 16
SHAPEIT SUPER EUR - SAS 0 -0.0031985 0.0003237 635.1038 -9.8802303 0.0000000 16
Beagle SUPER AFR - AMR 0 -0.0014479 0.0002472 628.8503 -5.8566941 0.0000001 17
Beagle SUPER AFR - EAS 0 -0.0056484 0.0003065 628.8503 -18.4294160 0.0000000 17
Beagle SUPER AFR - EUR 0 -0.0011418 0.0002670 628.8503 -4.2757689 0.0002130 17
Beagle SUPER AFR - SAS 0 -0.0041924 0.0002887 628.8503 -14.5208586 0.0000000 17
Beagle SUPER AMR - EAS 0 -0.0042004 0.0003248 628.8503 -12.9316463 0.0000000 17
Beagle SUPER AMR - EUR 0 0.0003061 0.0002879 628.8503 1.0632881 0.8252635 17
Beagle SUPER AMR - SAS 0 -0.0027445 0.0003081 628.8503 -8.9075221 0.0000000 17
Beagle SUPER EAS - EUR 0 0.0045066 0.0003401 628.8503 13.2489718 0.0000000 17
Beagle SUPER EAS - SAS 0 0.0014560 0.0003574 628.8503 4.0736608 0.0004995 17
Beagle SUPER EUR - SAS 0 -0.0030506 0.0003242 628.8503 -9.4089123 0.0000000 17
Eagle SUPER AFR - AMR 0 -0.0017465 0.0002472 628.8503 -7.0645036 0.0000000 17
Eagle SUPER AFR - EAS 0 -0.0061128 0.0003065 628.8503 -19.9446338 0.0000000 17
Eagle SUPER AFR - EUR 0 -0.0015395 0.0002670 628.8503 -5.7651733 0.0000001 17
Eagle SUPER AFR - SAS 0 -0.0045982 0.0002887 628.8503 -15.9262824 0.0000000 17
Eagle SUPER AMR - EAS 0 -0.0043662 0.0003248 628.8503 -13.4420597 0.0000000 17
Eagle SUPER AMR - EUR 0 0.0002070 0.0002879 628.8503 0.7189578 0.9521363 17
Eagle SUPER AMR - SAS 0 -0.0028516 0.0003081 628.8503 -9.2553411 0.0000000 17
Eagle SUPER EAS - EUR 0 0.0045732 0.0003401 628.8503 13.4449481 0.0000000 17
Eagle SUPER EAS - SAS 0 0.0015146 0.0003574 628.8503 4.2376915 0.0002508 17
Eagle SUPER EUR - SAS 0 -0.0030586 0.0003242 628.8503 -9.4336907 0.0000000 17
SHAPEIT SUPER AFR - AMR 0 -0.0014701 0.0002472 628.8503 -5.9463243 0.0000000 17
SHAPEIT SUPER AFR - EAS 0 -0.0056849 0.0003065 628.8503 -18.5484581 0.0000000 17
SHAPEIT SUPER AFR - EUR 0 -0.0009867 0.0002670 628.8503 -3.6947700 0.0022204 17
SHAPEIT SUPER AFR - SAS 0 -0.0043024 0.0002887 628.8503 -14.9019417 0.0000000 17
SHAPEIT SUPER AMR - EAS 0 -0.0042148 0.0003248 628.8503 -12.9757506 0.0000000 17
SHAPEIT SUPER AMR - EUR 0 0.0004834 0.0002879 628.8503 1.6791685 0.4476166 17
SHAPEIT SUPER AMR - SAS 0 -0.0028323 0.0003081 628.8503 -9.1927013 0.0000000 17
SHAPEIT SUPER EAS - EUR 0 0.0046982 0.0003401 628.8503 13.8123685 0.0000000 17
SHAPEIT SUPER EAS - SAS 0 0.0013824 0.0003574 628.8503 3.8679043 0.0011428 17
SHAPEIT SUPER EUR - SAS 0 -0.0033158 0.0003242 628.8503 -10.2267934 0.0000000 17
Beagle SUPER AFR - AMR 0 -0.0015084 0.0001993 629.0274 -7.5676517 0.0000000 18
Beagle SUPER AFR - EAS 0 -0.0047960 0.0002471 629.0274 -19.4097899 0.0000000 18
Beagle SUPER AFR - EUR 0 -0.0011030 0.0002153 629.0274 -5.1233338 0.0000040 18
Beagle SUPER AFR - SAS 0 -0.0036308 0.0002328 629.0274 -15.5986571 0.0000000 18
Beagle SUPER AMR - EAS 0 -0.0032877 0.0002619 629.0274 -12.5544450 0.0000000 18
Beagle SUPER AMR - EUR 0 0.0004053 0.0002321 629.0274 1.7463725 0.4062741 18
Beagle SUPER AMR - SAS 0 -0.0021225 0.0002484 629.0274 -8.5446072 0.0000000 18
Beagle SUPER EAS - EUR 0 0.0036930 0.0002742 629.0274 13.4669262 0.0000000 18
Beagle SUPER EAS - SAS 0 0.0011652 0.0002881 629.0274 4.0437078 0.0005649 18
Beagle SUPER EUR - SAS 0 -0.0025278 0.0002614 629.0274 -9.6705886 0.0000000 18
Eagle SUPER AFR - AMR 0 -0.0018831 0.0001993 629.0274 -9.4479626 0.0000000 18
Eagle SUPER AFR - EAS 0 -0.0054796 0.0002471 629.0274 -22.1761324 0.0000000 18
Eagle SUPER AFR - EUR 0 -0.0016680 0.0002153 629.0274 -7.7474975 0.0000000 18
Eagle SUPER AFR - SAS 0 -0.0039868 0.0002328 629.0274 -17.1281809 0.0000000 18
Eagle SUPER AMR - EAS 0 -0.0035964 0.0002619 629.0274 -13.7335174 0.0000000 18
Eagle SUPER AMR - EUR 0 0.0002152 0.0002321 629.0274 0.9269811 0.8864313 18
Eagle SUPER AMR - SAS 0 -0.0021037 0.0002484 629.0274 -8.4690977 0.0000000 18
Eagle SUPER EAS - EUR 0 0.0038116 0.0002742 629.0274 13.8993445 0.0000000 18
Eagle SUPER EAS - SAS 0 0.0014927 0.0002881 629.0274 5.1803522 0.0000030 18
Eagle SUPER EUR - SAS 0 -0.0023189 0.0002614 629.0274 -8.8712456 0.0000000 18
SHAPEIT SUPER AFR - AMR 0 -0.0016083 0.0001993 629.0274 -8.0689797 0.0000000 18
SHAPEIT SUPER AFR - EAS 0 -0.0048672 0.0002471 629.0274 -19.6978321 0.0000000 18
SHAPEIT SUPER AFR - EUR 0 -0.0009872 0.0002153 629.0274 -4.5852150 0.0000536 18
SHAPEIT SUPER AFR - SAS 0 -0.0037775 0.0002328 629.0274 -16.2286496 0.0000000 18
SHAPEIT SUPER AMR - EAS 0 -0.0032589 0.0002619 629.0274 -12.4446596 0.0000000 18
SHAPEIT SUPER AMR - EUR 0 0.0006211 0.0002321 629.0274 2.6760167 0.0586925 18
SHAPEIT SUPER AMR - SAS 0 -0.0021692 0.0002484 629.0274 -8.7326821 0.0000000 18
SHAPEIT SUPER EAS - EUR 0 0.0038800 0.0002742 629.0274 14.1489358 0.0000000 18
SHAPEIT SUPER EAS - SAS 0 0.0010897 0.0002881 629.0274 3.7818038 0.0015960 18
SHAPEIT SUPER EUR - SAS 0 -0.0027903 0.0002614 629.0274 -10.6748020 0.0000000 18
Beagle SUPER AFR - AMR 0 -0.0013213 0.0002242 634.4979 -5.8929134 0.0000001 19
Beagle SUPER AFR - EAS 0 -0.0050518 0.0002780 634.4979 -18.1740966 0.0000000 19
Beagle SUPER AFR - EUR 0 -0.0009680 0.0002422 634.4979 -3.9968421 0.0006830 19
Beagle SUPER AFR - SAS 0 -0.0035872 0.0002618 634.4979 -13.6997028 0.0000000 19
Beagle SUPER AMR - EAS 0 -0.0037304 0.0002946 634.4979 -12.6631694 0.0000000 19
Beagle SUPER AMR - EUR 0 0.0003533 0.0002611 634.4979 1.3531124 0.6579387 19
Beagle SUPER AMR - SAS 0 -0.0022659 0.0002794 634.4979 -8.1089849 0.0000000 19
Beagle SUPER EAS - EUR 0 0.0040838 0.0003085 634.4979 13.2378978 0.0000000 19
Beagle SUPER EAS - SAS 0 0.0014645 0.0003242 634.4979 4.5180460 0.0000728 19
Beagle SUPER EUR - SAS 0 -0.0026192 0.0002941 634.4979 -8.9074205 0.0000000 19
Eagle SUPER AFR - AMR 0 -0.0017241 0.0002242 634.4979 -7.6891767 0.0000000 19
Eagle SUPER AFR - EAS 0 -0.0055256 0.0002780 634.4979 -19.8788073 0.0000000 19
Eagle SUPER AFR - EUR 0 -0.0013803 0.0002422 634.4979 -5.6990356 0.0000002 19
Eagle SUPER AFR - SAS 0 -0.0038162 0.0002618 634.4979 -14.5740844 0.0000000 19
Eagle SUPER AMR - EAS 0 -0.0038015 0.0002946 634.4979 -12.9044968 0.0000000 19
Eagle SUPER AMR - EUR 0 0.0003438 0.0002611 634.4979 1.3167309 0.6808961 19
Eagle SUPER AMR - SAS 0 -0.0020921 0.0002794 634.4979 -7.4870059 0.0000000 19
Eagle SUPER EAS - EUR 0 0.0041453 0.0003085 634.4979 13.4375588 0.0000000 19
Eagle SUPER EAS - SAS 0 0.0017094 0.0003242 634.4979 5.2735435 0.0000018 19
Eagle SUPER EUR - SAS 0 -0.0024359 0.0002941 634.4979 -8.2840530 0.0000000 19
SHAPEIT SUPER AFR - AMR 0 -0.0014333 0.0002242 634.4979 -6.3923738 0.0000000 19
SHAPEIT SUPER AFR - EAS 0 -0.0052570 0.0002780 634.4979 -18.9124522 0.0000000 19
SHAPEIT SUPER AFR - EUR 0 -0.0009033 0.0002422 634.4979 -3.7298200 0.0019443 19
SHAPEIT SUPER AFR - SAS 0 -0.0038854 0.0002618 634.4979 -14.8386242 0.0000000 19
SHAPEIT SUPER AMR - EAS 0 -0.0038237 0.0002946 634.4979 -12.9797041 0.0000000 19
SHAPEIT SUPER AMR - EUR 0 0.0005300 0.0002611 634.4979 2.0296942 0.2529362 19
SHAPEIT SUPER AMR - SAS 0 -0.0024522 0.0002794 634.4979 -8.7754567 0.0000000 19
SHAPEIT SUPER EAS - EUR 0 0.0043537 0.0003085 634.4979 14.1128280 0.0000000 19
SHAPEIT SUPER EAS - SAS 0 0.0013715 0.0003242 634.4979 4.2311831 0.0002576 19
SHAPEIT SUPER EUR - SAS 0 -0.0029821 0.0002941 634.4979 -10.1415417 0.0000000 19
Beagle SUPER AFR - AMR 0 -0.0017747 0.0002477 624.9958 -7.1648970 0.0000000 20
Beagle SUPER AFR - EAS 0 -0.0057185 0.0003071 624.9958 -18.6226969 0.0000000 20
Beagle SUPER AFR - EUR 0 -0.0010484 0.0002676 624.9958 -3.9184499 0.0009367 20
Beagle SUPER AFR - SAS 0 -0.0040930 0.0002893 624.9958 -14.1496900 0.0000000 20
Beagle SUPER AMR - EAS 0 -0.0039438 0.0003254 624.9958 -12.1183187 0.0000000 20
Beagle SUPER AMR - EUR 0 0.0007263 0.0002884 624.9958 2.5181183 0.0879064 20
Beagle SUPER AMR - SAS 0 -0.0023183 0.0003087 624.9958 -7.5100060 0.0000000 20
Beagle SUPER EAS - EUR 0 0.0046701 0.0003408 624.9958 13.7036535 0.0000000 20
Beagle SUPER EAS - SAS 0 0.0016255 0.0003581 624.9958 4.5392309 0.0000663 20
Beagle SUPER EUR - SAS 0 -0.0030446 0.0003248 624.9958 -9.3726940 0.0000000 20
Eagle SUPER AFR - AMR 0 -0.0021922 0.0002477 624.9958 -8.8501815 0.0000000 20
Eagle SUPER AFR - EAS 0 -0.0063671 0.0003071 624.9958 -20.7348940 0.0000000 20
Eagle SUPER AFR - EUR 0 -0.0015824 0.0002676 624.9958 -5.9145031 0.0000001 20
Eagle SUPER AFR - SAS 0 -0.0044268 0.0002893 624.9958 -15.3035387 0.0000000 20
Eagle SUPER AMR - EAS 0 -0.0041749 0.0003254 624.9958 -12.8286031 0.0000000 20
Eagle SUPER AMR - EUR 0 0.0006097 0.0002884 624.9958 2.1138627 0.2153785 20
Eagle SUPER AMR - SAS 0 -0.0022346 0.0003087 624.9958 -7.2389551 0.0000000 20
Eagle SUPER EAS - EUR 0 0.0047846 0.0003408 624.9958 14.0397749 0.0000000 20
Eagle SUPER EAS - SAS 0 0.0019403 0.0003581 624.9958 5.4184029 0.0000009 20
Eagle SUPER EUR - SAS 0 -0.0028444 0.0003248 624.9958 -8.7561534 0.0000000 20
SHAPEIT SUPER AFR - AMR 0 -0.0019839 0.0002477 624.9958 -8.0095161 0.0000000 20
SHAPEIT SUPER AFR - EAS 0 -0.0059898 0.0003071 624.9958 -19.5063328 0.0000000 20
SHAPEIT SUPER AFR - EUR 0 -0.0010475 0.0002676 624.9958 -3.9152178 0.0009488 20
SHAPEIT SUPER AFR - SAS 0 -0.0043254 0.0002893 624.9958 -14.9529285 0.0000000 20
SHAPEIT SUPER AMR - EAS 0 -0.0040059 0.0003254 624.9958 -12.3092271 0.0000000 20
SHAPEIT SUPER AMR - EUR 0 0.0009364 0.0002884 624.9958 3.2464170 0.0107676 20
SHAPEIT SUPER AMR - SAS 0 -0.0023414 0.0003087 624.9958 -7.5849650 0.0000000 20
SHAPEIT SUPER EAS - EUR 0 0.0049423 0.0003408 624.9958 14.5023907 0.0000000 20
SHAPEIT SUPER EAS - SAS 0 0.0016645 0.0003581 624.9958 4.6481116 0.0000401 20
SHAPEIT SUPER EUR - SAS 0 -0.0032778 0.0003248 624.9958 -10.0906273 0.0000000 20
Beagle SUPER AFR - AMR 0 -0.0007372 0.0002263 643.1741 -3.2576924 0.0103616 21
Beagle SUPER AFR - EAS 0 -0.0036969 0.0002806 643.1741 -13.1770282 0.0000000 21
Beagle SUPER AFR - EUR 0 -0.0003914 0.0002444 643.1741 -1.6011994 0.4971217 21
Beagle SUPER AFR - SAS 0 -0.0028476 0.0002643 643.1741 -10.7746926 0.0000000 21
Beagle SUPER AMR - EAS 0 -0.0029596 0.0002973 643.1741 -9.9538464 0.0000000 21
Beagle SUPER AMR - EUR 0 0.0003458 0.0002635 643.1741 1.3122716 0.6836824 21
Beagle SUPER AMR - SAS 0 -0.0021104 0.0002820 643.1741 -7.4825790 0.0000000 21
Beagle SUPER EAS - EUR 0 0.0033054 0.0003114 643.1741 10.6160764 0.0000000 21
Beagle SUPER EAS - SAS 0 0.0008493 0.0003272 643.1741 2.5957829 0.0723010 21
Beagle SUPER EUR - SAS 0 -0.0024562 0.0002968 643.1741 -8.2758864 0.0000000 21
Eagle SUPER AFR - AMR 0 -0.0011533 0.0002263 643.1741 -5.0959624 0.0000045 21
Eagle SUPER AFR - EAS 0 -0.0042066 0.0002806 643.1741 -14.9940614 0.0000000 21
Eagle SUPER AFR - EUR 0 -0.0008309 0.0002444 643.1741 -3.3992532 0.0064259 21
Eagle SUPER AFR - SAS 0 -0.0032272 0.0002643 643.1741 -12.2111418 0.0000000 21
Eagle SUPER AMR - EAS 0 -0.0030534 0.0002973 643.1741 -10.2691848 0.0000000 21
Eagle SUPER AMR - EUR 0 0.0003223 0.0002635 643.1741 1.2230462 0.7379489 21
Eagle SUPER AMR - SAS 0 -0.0020740 0.0002820 643.1741 -7.3535865 0.0000000 21
Eagle SUPER EAS - EUR 0 0.0033757 0.0003114 643.1741 10.8416870 0.0000000 21
Eagle SUPER EAS - SAS 0 0.0009794 0.0003272 643.1741 2.9935632 0.0238569 21
Eagle SUPER EUR - SAS 0 -0.0023963 0.0002968 643.1741 -8.0740772 0.0000000 21
SHAPEIT SUPER AFR - AMR 0 -0.0008927 0.0002263 643.1741 -3.9446457 0.0008415 21
SHAPEIT SUPER AFR - EAS 0 -0.0037265 0.0002806 643.1741 -13.2827307 0.0000000 21
SHAPEIT SUPER AFR - EUR 0 -0.0003472 0.0002444 643.1741 -1.4202424 0.6147922 21
SHAPEIT SUPER AFR - SAS 0 -0.0030795 0.0002643 643.1741 -11.6520154 0.0000000 21
SHAPEIT SUPER AMR - EAS 0 -0.0028338 0.0002973 643.1741 -9.5307290 0.0000000 21
SHAPEIT SUPER AMR - EUR 0 0.0005455 0.0002635 643.1741 2.0700286 0.2344216 21
SHAPEIT SUPER AMR - SAS 0 -0.0021868 0.0002820 643.1741 -7.7534713 0.0000000 21
SHAPEIT SUPER EAS - EUR 0 0.0033793 0.0003114 643.1741 10.8533863 0.0000000 21
SHAPEIT SUPER EAS - SAS 0 0.0006471 0.0003272 643.1741 1.9777273 0.2780590 21
SHAPEIT SUPER EUR - SAS 0 -0.0027323 0.0002968 643.1741 -9.2061716 0.0000000 21
Beagle SUPER AFR - AMR 0 -0.0010292 0.0002758 635.3619 -3.7317389 0.0019300 22
Beagle SUPER AFR - EAS 0 -0.0049191 0.0003419 635.3619 -14.3868553 0.0000000 22
Beagle SUPER AFR - EUR 0 -0.0006473 0.0002979 635.3619 -2.1726565 0.1914428 22
Beagle SUPER AFR - SAS 0 -0.0036761 0.0003221 635.3619 -11.4131038 0.0000000 22
Beagle SUPER AMR - EAS 0 -0.0038899 0.0003624 635.3619 -10.7345867 0.0000000 22
Beagle SUPER AMR - EUR 0 0.0003820 0.0003212 635.3619 1.1892886 0.7575832 22
Beagle SUPER AMR - SAS 0 -0.0026468 0.0003437 635.3619 -7.7004335 0.0000000 22
Beagle SUPER EAS - EUR 0 0.0042718 0.0003795 635.3619 11.2575478 0.0000000 22
Beagle SUPER EAS - SAS 0 0.0012430 0.0003987 635.3619 3.1175250 0.0162906 22
Beagle SUPER EUR - SAS 0 -0.0030288 0.0003617 635.3619 -8.3737080 0.0000000 22
Eagle SUPER AFR - AMR 0 -0.0013812 0.0002758 635.3619 -5.0079467 0.0000071 22
Eagle SUPER AFR - EAS 0 -0.0055010 0.0003419 635.3619 -16.0887347 0.0000000 22
Eagle SUPER AFR - EUR 0 -0.0010241 0.0002979 635.3619 -3.4377523 0.0056263 22
Eagle SUPER AFR - SAS 0 -0.0039851 0.0003221 635.3619 -12.3727089 0.0000000 22
Eagle SUPER AMR - EAS 0 -0.0041198 0.0003624 635.3619 -11.3690675 0.0000000 22
Eagle SUPER AMR - EUR 0 0.0003571 0.0003212 635.3619 1.1117540 0.8003720 22
Eagle SUPER AMR - SAS 0 -0.0026039 0.0003437 635.3619 -7.5756091 0.0000000 22
Eagle SUPER EAS - EUR 0 0.0044769 0.0003795 635.3619 11.7978168 0.0000000 22
Eagle SUPER EAS - SAS 0 0.0015159 0.0003987 635.3619 3.8017516 0.0014768 22
Eagle SUPER EUR - SAS 0 -0.0029610 0.0003617 635.3619 -8.1862407 0.0000000 22
SHAPEIT SUPER AFR - AMR 0 -0.0011736 0.0002758 635.3619 -4.2550574 0.0002325 22
SHAPEIT SUPER AFR - EAS 0 -0.0049986 0.0003419 635.3619 -14.6193366 0.0000000 22
SHAPEIT SUPER AFR - EUR 0 -0.0006805 0.0002979 635.3619 -2.2843712 0.1512505 22
SHAPEIT SUPER AFR - SAS 0 -0.0039901 0.0003221 635.3619 -12.3882304 0.0000000 22
SHAPEIT SUPER AMR - EAS 0 -0.0038250 0.0003624 635.3619 -10.5556388 0.0000000 22
SHAPEIT SUPER AMR - EUR 0 0.0004930 0.0003212 635.3619 1.5350562 0.5399803 22
SHAPEIT SUPER AMR - SAS 0 -0.0028166 0.0003437 635.3619 -8.1942754 0.0000000 22
SHAPEIT SUPER EAS - EUR 0 0.0043180 0.0003795 635.3619 11.3793193 0.0000000 22
SHAPEIT SUPER EAS - SAS 0 0.0010085 0.0003987 635.3619 2.5291789 0.0855157 22
SHAPEIT SUPER EUR - SAS 0 -0.0033096 0.0003617 635.3619 -9.1500304 0.0000000 22
Beagle SUPER AFR - AMR 0 -0.0004255 0.0000910 1048.8670 -4.6761548 0.0000325 23
Beagle SUPER AFR - EAS 0 -0.0028946 0.0000910 1048.8670 -31.8102658 0.0000000 23
Beagle SUPER AFR - EUR 0 -0.0008571 0.0000910 1048.8670 -9.4193721 0.0000000 23
Beagle SUPER AFR - SAS 0 -0.0017394 0.0000910 1048.8670 -19.1148049 0.0000000 23
Beagle SUPER AMR - EAS 0 -0.0024691 0.0000910 1048.8670 -27.1341110 0.0000000 23
Beagle SUPER AMR - EUR 0 -0.0004316 0.0000910 1048.8670 -4.7432172 0.0000236 23
Beagle SUPER AMR - SAS 0 -0.0013139 0.0000910 1048.8670 -14.4386500 0.0000000 23
Beagle SUPER EAS - EUR 0 0.0020375 0.0000910 1048.8670 22.3908937 0.0000000 23
Beagle SUPER EAS - SAS 0 0.0011552 0.0000910 1048.8670 12.6954609 0.0000000 23
Beagle SUPER EUR - SAS 0 -0.0008822 0.0000910 1048.8670 -9.6954328 0.0000000 23
Eagle SUPER AFR - AMR 0 -0.0004013 0.0000910 1048.8670 -4.4099380 0.0001112 23
Eagle SUPER AFR - EAS 0 -0.0032492 0.0000910 1048.8670 -35.7067602 0.0000000 23
Eagle SUPER AFR - EUR 0 -0.0009391 0.0000910 1048.8670 -10.3203979 0.0000000 23
Eagle SUPER AFR - SAS 0 -0.0019586 0.0000910 1048.8670 -21.5237585 0.0000000 23
Eagle SUPER AMR - EAS 0 -0.0028479 0.0000910 1048.8670 -31.2968222 0.0000000 23
Eagle SUPER AMR - EUR 0 -0.0005378 0.0000910 1048.8670 -5.9104599 0.0000000 23
Eagle SUPER AMR - SAS 0 -0.0015573 0.0000910 1048.8670 -17.1138205 0.0000000 23
Eagle SUPER EAS - EUR 0 0.0023101 0.0000910 1048.8670 25.3863622 0.0000000 23
Eagle SUPER EAS - SAS 0 0.0012906 0.0000910 1048.8670 14.1830017 0.0000000 23
Eagle SUPER EUR - SAS 0 -0.0010195 0.0000910 1048.8670 -11.2033606 0.0000000 23
SHAPEIT SUPER AFR - AMR 0 -0.0004491 0.0000910 1048.8670 -4.9351372 0.0000092 23
SHAPEIT SUPER AFR - EAS 0 -0.0027998 0.0000910 1048.8670 -30.7685457 0.0000000 23
SHAPEIT SUPER AFR - EUR 0 -0.0008528 0.0000910 1048.8670 -9.3721252 0.0000000 23
SHAPEIT SUPER AFR - SAS 0 -0.0016975 0.0000910 1048.8670 -18.6541676 0.0000000 23
SHAPEIT SUPER AMR - EAS 0 -0.0023507 0.0000910 1048.8670 -25.8334085 0.0000000 23
SHAPEIT SUPER AMR - EUR 0 -0.0004037 0.0000910 1048.8670 -4.4369880 0.0000984 23
SHAPEIT SUPER AMR - SAS 0 -0.0012484 0.0000910 1048.8670 -13.7190304 0.0000000 23
SHAPEIT SUPER EAS - EUR 0 0.0019470 0.0000910 1048.8670 21.3964205 0.0000000 23
SHAPEIT SUPER EAS - SAS 0 0.0011024 0.0000910 1048.8670 12.1143781 0.0000000 23
SHAPEIT SUPER EUR - SAS 0 -0.0008446 0.0000910 1048.8670 -9.2820424 0.0000000 23

Switch Errors

Next, let’s consider switches and flips independently:

# df_switches <- df_switch_trio[[1]] %>%
#   mutate(Eagle = (n_other_eagle) / n_hets,
#          Beagle = (n_other_beagle) / n_hets,
#          SHAPEIT = (n_other_shapeit) / n_hets) %>%
#   select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#   mutate(chrom = 1)
# 
# for(i in 2:22){
#   df_switches <- bind_rows(df_switches, 
#                         {
#                           df_switch_trio[[i]] %>%
#                             mutate(Eagle = (n_other_eagle) / n_hets,
#                                    Beagle = (n_other_beagle) / n_hets,
#                                    SHAPEIT = (n_other_shapeit) / n_hets) %>%
#                             select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#                             mutate(chrom = i)
#                         })
# }
# 


df_switches <- df_switch_trio_noth %>%
  mutate(Eagle = (n_switch_e) / n_het,
         Beagle = (n_switch_b) / n_het,
         SHAPEIT = (n_switch_s) / n_het) %>%
  select(Eagle, Beagle, SHAPEIT, sample, chrom)

df_switches <- df_switches %>%
  left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
  rename(pair_id = sample) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)

df_switches <- df_switches %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_other_eagle) / n_hets,
                                   Beagle = (n_other_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

df_switches %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  knitr::kable()
chrom Beagle Eagle SHAPEIT
1 0.0019084 0.0024999 0.0018737
2 0.0017862 0.0023895 0.0017640
3 0.0016596 0.0022318 0.0016561
4 0.0015058 0.0020500 0.0014972
5 0.0016545 0.0022052 0.0016464
6 0.0014645 0.0019622 0.0014465
7 0.0018935 0.0024565 0.0018503
8 0.0016766 0.0022457 0.0016720
9 0.0025877 0.0031912 0.0025272
10 0.0018561 0.0024419 0.0018115
11 0.0017216 0.0023083 0.0016987
12 0.0018425 0.0024028 0.0018366
13 0.0017893 0.0023635 0.0017801
14 0.0021114 0.0027364 0.0021083
15 0.0027363 0.0034055 0.0027022
16 0.0025976 0.0033503 0.0025877
17 0.0027715 0.0035106 0.0027148
18 0.0020664 0.0026810 0.0020536
19 0.0027082 0.0033871 0.0026400
20 0.0027694 0.0034397 0.0026885
21 0.0032355 0.0038173 0.0032186
22 0.0038186 0.0045225 0.0036899
23 0.0017000 0.0022896 0.0015654
df_switches %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%  
  knitr::kable() 
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
chrom SUPER Beagle Eagle SHAPEIT
1 AFR 0.0013031 0.0017879 0.0012370
1 AMR 0.0017838 0.0023339 0.0017660
1 EAS 0.0031973 0.0041090 0.0032297
1 EUR 0.0017845 0.0023154 0.0017281
1 SAS 0.0026048 0.0033203 0.0025879
2 AFR 0.0012032 0.0017167 0.0011570
2 AMR 0.0017330 0.0023111 0.0017309
2 EAS 0.0030258 0.0038904 0.0030452
2 EUR 0.0015921 0.0021094 0.0015504
2 SAS 0.0024448 0.0031883 0.0024363
3 AFR 0.0011096 0.0016027 0.0010764
3 AMR 0.0015866 0.0021087 0.0015880
3 EAS 0.0027729 0.0036531 0.0028329
3 EUR 0.0015385 0.0020425 0.0015186
3 SAS 0.0022871 0.0029521 0.0023130
4 AFR 0.0009938 0.0014277 0.0009428
4 AMR 0.0015003 0.0020231 0.0015086
4 EAS 0.0024240 0.0032640 0.0025213
4 EUR 0.0013769 0.0018891 0.0013453
4 SAS 0.0021102 0.0027394 0.0021138
5 AFR 0.0010981 0.0015620 0.0010441
5 AMR 0.0015576 0.0020605 0.0016006
5 EAS 0.0027997 0.0036286 0.0028362
5 EUR 0.0015035 0.0020003 0.0014763
5 SAS 0.0023465 0.0030116 0.0023506
6 AFR 0.0010003 0.0014310 0.0009608
6 AMR 0.0013976 0.0018431 0.0013981
6 EAS 0.0024011 0.0031797 0.0024318
6 EUR 0.0013123 0.0017258 0.0012665
6 SAS 0.0020679 0.0026763 0.0020650
7 AFR 0.0013913 0.0018807 0.0013021
7 AMR 0.0017797 0.0022894 0.0017757
7 EAS 0.0030445 0.0038232 0.0030652
7 EUR 0.0017074 0.0022170 0.0016397
7 SAS 0.0025239 0.0032315 0.0025031
8 AFR 0.0010952 0.0015763 0.0010574
8 AMR 0.0016408 0.0021809 0.0016906
8 EAS 0.0028758 0.0037101 0.0028902
8 EUR 0.0015261 0.0020471 0.0015018
8 SAS 0.0022823 0.0029429 0.0022780
9 AFR 0.0019710 0.0024755 0.0018571
9 AMR 0.0023622 0.0029090 0.0023513
9 EAS 0.0039947 0.0049926 0.0040020
9 EUR 0.0024834 0.0030163 0.0024100
9 SAS 0.0033491 0.0040325 0.0032937
10 AFR 0.0013054 0.0018014 0.0012220
10 AMR 0.0017613 0.0023007 0.0017395
10 EAS 0.0029666 0.0038215 0.0030032
10 EUR 0.0017012 0.0022140 0.0016233
10 SAS 0.0025656 0.0033022 0.0025487
11 AFR 0.0011327 0.0016113 0.0010900
11 AMR 0.0016660 0.0022169 0.0016743
11 EAS 0.0028719 0.0037021 0.0028828
11 EUR 0.0015605 0.0021015 0.0015069
11 SAS 0.0024324 0.0031835 0.0024156
12 AFR 0.0012347 0.0016935 0.0011711
12 AMR 0.0017109 0.0022619 0.0017431
12 EAS 0.0030297 0.0038845 0.0030974
12 EUR 0.0016848 0.0022047 0.0016367
12 SAS 0.0026850 0.0033016 0.0027443
13 AFR 0.0012374 0.0016608 0.0011887
13 AMR 0.0016338 0.0021985 0.0016718
13 EAS 0.0030470 0.0038889 0.0030357
13 EUR 0.0016449 0.0021782 0.0016133
13 SAS 0.0024617 0.0032325 0.0024994
14 AFR 0.0015135 0.0020048 0.0014646
14 AMR 0.0020288 0.0026707 0.0020724
14 EAS 0.0033255 0.0042777 0.0033896
14 EUR 0.0019515 0.0025040 0.0019100
14 SAS 0.0028314 0.0035589 0.0028525
15 AFR 0.0020558 0.0026301 0.0019531
15 AMR 0.0024911 0.0031218 0.0025112
15 EAS 0.0042257 0.0051794 0.0042498
15 EUR 0.0026587 0.0032128 0.0025716
15 SAS 0.0035765 0.0044363 0.0036347
16 AFR 0.0018445 0.0025092 0.0017355
16 AMR 0.0024940 0.0031937 0.0025249
16 EAS 0.0041844 0.0052628 0.0042751
16 EUR 0.0023658 0.0031430 0.0024116
16 SAS 0.0034933 0.0042329 0.0034969
17 AFR 0.0019400 0.0025814 0.0018683
17 AMR 0.0025915 0.0032833 0.0025548
17 EAS 0.0045569 0.0055374 0.0046059
17 EUR 0.0025843 0.0032542 0.0025085
17 SAS 0.0037514 0.0046797 0.0036319
18 AFR 0.0013736 0.0018761 0.0013308
18 AMR 0.0019493 0.0025107 0.0019493
18 EAS 0.0034908 0.0044029 0.0035391
18 EUR 0.0019470 0.0025446 0.0019378
18 SAS 0.0028371 0.0035722 0.0028183
19 AFR 0.0019787 0.0026070 0.0018653
19 AMR 0.0025439 0.0031896 0.0024700
19 EAS 0.0043873 0.0053070 0.0043948
19 EUR 0.0025013 0.0031173 0.0024208
19 SAS 0.0035366 0.0042639 0.0035355
20 AFR 0.0019127 0.0025023 0.0017881
20 AMR 0.0026849 0.0033720 0.0026430
20 EAS 0.0046822 0.0055716 0.0046542
20 EUR 0.0025032 0.0030775 0.0024023
20 SAS 0.0036461 0.0044155 0.0035863
21 AFR 0.0027883 0.0032811 0.0027103
21 AMR 0.0030047 0.0035338 0.0030654
21 EAS 0.0044825 0.0052999 0.0044698
21 EUR 0.0029705 0.0035425 0.0029284
21 SAS 0.0039422 0.0046324 0.0039729
22 AFR 0.0030976 0.0037686 0.0028908
22 AMR 0.0035044 0.0041885 0.0034282
22 EAS 0.0056296 0.0065746 0.0054882
22 EUR 0.0035995 0.0041890 0.0035406
22 SAS 0.0047719 0.0055252 0.0046662
23 AFR 0.0008880 0.0013558 0.0007707
23 AMR 0.0012206 0.0016760 0.0011439
23 EAS 0.0028352 0.0036614 0.0026536
23 EUR 0.0015108 0.0020636 0.0013951
23 SAS 0.0020451 0.0026914 0.0018639
df_switches %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Switch Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_switches$chrom)), breaks = unique(df_switches$chrom))

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
df_switches %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Switch Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_switches$chrom)), breaks = unique(df_switches$chrom))
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
mod_b <- df_switches %>%
  select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
  {lmerTest::lmer(Beagle ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_b) %>% broom::tidy()
# A tibble: 1 × 7
  term            sumsq   meansq NumDF DenDF statistic p.value
  <chr>           <dbl>    <dbl> <int> <dbl>     <dbl>   <dbl>
1 factor(chrom) 0.00490 0.000223    22 9521.     1092.       0
emmeans::emmeans(mod_b, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
  separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
  filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>% 
  knitr::kable()
term chrom1 chrom2 null.value estimate std.error df statistic adj.p.value
chrom chrom1 chrom23 0 0.0002085 4.79e-05 1997.721 4.3518930 0.0030782
chrom chrom2 chrom23 0 0.0000862 4.79e-05 1997.721 1.8000017 0.9797694
chrom chrom3 chrom23 0 -0.0000404 4.79e-05 1997.721 -0.8433140 0.9999999
chrom chrom4 chrom23 0 -0.0001941 4.79e-05 1997.721 -4.0528337 0.0105070
chrom chrom5 chrom23 0 -0.0000454 4.79e-05 1997.721 -0.9487342 0.9999991
chrom chrom6 chrom23 0 -0.0002355 4.79e-05 1997.721 -4.9167873 0.0002260
chrom chrom7 chrom23 0 0.0001936 4.79e-05 1997.721 4.0408783 0.0110090
chrom chrom8 chrom23 0 -0.0000234 4.79e-05 1997.721 -0.4886566 1.0000000
chrom chrom9 chrom23 0 0.0008878 4.79e-05 1997.721 18.5333599 0.0000000
chrom chrom10 chrom23 0 0.0001561 4.79e-05 1997.721 3.2595434 0.1477995
chrom chrom11 chrom23 0 0.0000217 4.79e-05 1997.721 0.4521216 1.0000000
chrom chrom12 chrom23 0 0.0001425 4.79e-05 1997.721 2.9758272 0.2947120
chrom chrom13 chrom23 0 0.0000894 4.79e-05 1997.721 1.8659699 0.9696929
chrom chrom14 chrom23 0 0.0004115 4.79e-05 1997.721 8.5899605 0.0000000
chrom chrom15 chrom23 0 0.0010363 4.79e-05 1997.721 21.6344847 0.0000000
chrom chrom16 chrom23 0 0.0008977 4.79e-05 1997.721 18.7400917 0.0000000
chrom chrom17 chrom23 0 0.0010716 4.79e-05 1997.721 22.3708948 0.0000000
chrom chrom18 chrom23 0 0.0003664 4.79e-05 1997.721 7.6499754 0.0000000
chrom chrom19 chrom23 0 0.0010083 4.79e-05 1997.721 21.0494934 0.0000000
chrom chrom20 chrom23 0 0.0010694 4.79e-05 1997.721 22.3259912 0.0000000
chrom chrom21 chrom23 0 0.0015355 4.79e-05 1997.721 32.0565019 0.0000000
chrom chrom22 chrom23 0 0.0021187 4.79e-05 1997.721 44.2305362 0.0000000
mod_e <- df_switches %>%
  select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
  {lmerTest::lmer(Eagle ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_e) %>% broom::tidy()
# A tibble: 1 × 7
  term            sumsq   meansq NumDF DenDF statistic p.value
  <chr>           <dbl>    <dbl> <int> <dbl>     <dbl>   <dbl>
1 factor(chrom) 0.00571 0.000259    22 9467.     1191.       0
emmeans::emmeans(mod_e, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
  separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
  filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>% 
  knitr::kable()
term chrom1 chrom2 null.value estimate std.error df statistic adj.p.value
chrom chrom1 chrom23 0 0.0002103 5.47e-05 1900.994 3.8420012 0.0232835
chrom chrom2 chrom23 0 0.0000999 5.47e-05 1900.994 1.8253984 0.9762487
chrom chrom3 chrom23 0 -0.0000578 5.47e-05 1900.994 -1.0567801 0.9999933
chrom chrom4 chrom23 0 -0.0002396 5.47e-05 1900.994 -4.3775428 0.0027624
chrom chrom5 chrom23 0 -0.0000844 5.47e-05 1900.994 -1.5426689 0.9971521
chrom chrom6 chrom23 0 -0.0003275 5.47e-05 1900.994 -5.9834024 0.0000007
chrom chrom7 chrom23 0 0.0001669 5.47e-05 1900.994 3.0495519 0.2500202
chrom chrom8 chrom23 0 -0.0000439 5.47e-05 1900.994 -0.8019284 1.0000000
chrom chrom9 chrom23 0 0.0009016 5.47e-05 1900.994 16.4729705 0.0000000
chrom chrom10 chrom23 0 0.0001523 5.47e-05 1900.994 2.7819346 0.4316661
chrom chrom11 chrom23 0 0.0000187 5.47e-05 1900.994 0.3407932 1.0000000
chrom chrom12 chrom23 0 0.0001132 5.47e-05 1900.994 2.0684998 0.9146935
chrom chrom13 chrom23 0 0.0000739 5.47e-05 1900.994 1.3500220 0.9995989
chrom chrom14 chrom23 0 0.0004467 5.47e-05 1900.994 8.1626972 0.0000000
chrom chrom15 chrom23 0 0.0011159 5.47e-05 1900.994 20.3887982 0.0000000
chrom chrom16 chrom23 0 0.0010607 5.47e-05 1900.994 19.3807543 0.0000000
chrom chrom17 chrom23 0 0.0012209 5.47e-05 1900.994 22.3084662 0.0000000
chrom chrom18 chrom23 0 0.0003914 5.47e-05 1900.994 7.1510578 0.0000000
chrom chrom19 chrom23 0 0.0010975 5.47e-05 1900.994 20.0531651 0.0000000
chrom chrom20 chrom23 0 0.0011501 5.47e-05 1900.994 21.0134809 0.0000000
chrom chrom21 chrom23 0 0.0015277 5.47e-05 1900.994 27.9130811 0.0000000
chrom chrom22 chrom23 0 0.0022329 5.47e-05 1900.994 40.7981837 0.0000000
mod_s <- df_switches %>%
  select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
  {lmerTest::lmer(SHAPEIT ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_s) %>% broom::tidy()
# A tibble: 1 × 7
  term            sumsq   meansq NumDF DenDF statistic p.value
  <chr>           <dbl>    <dbl> <int> <dbl>     <dbl>   <dbl>
1 factor(chrom) 0.00457 0.000208    22 9600.      931.       0
emmeans::emmeans(mod_s, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
  separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
  filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>% 
  knitr::kable()
term chrom1 chrom2 null.value estimate std.error df statistic adj.p.value
chrom chrom1 chrom23 0 0.0003083 4.84e-05 2038.425 6.364209 0.0000001
chrom chrom2 chrom23 0 0.0001986 4.84e-05 2038.425 4.098871 0.0087573
chrom chrom3 chrom23 0 0.0000907 4.84e-05 2038.425 1.871582 0.9686901
chrom chrom4 chrom23 0 -0.0000682 4.84e-05 2038.425 -1.408091 0.9992386
chrom chrom5 chrom23 0 0.0000810 4.84e-05 2038.425 1.671210 0.9917721
chrom chrom6 chrom23 0 -0.0001189 4.84e-05 2038.425 -2.455000 0.6892273
chrom chrom7 chrom23 0 0.0002849 4.84e-05 2038.425 5.880450 0.0000012
chrom chrom8 chrom23 0 0.0001066 4.84e-05 2038.425 2.200602 0.8551050
chrom chrom9 chrom23 0 0.0009618 4.84e-05 2038.425 19.852729 0.0000000
chrom chrom10 chrom23 0 0.0002460 4.84e-05 2038.425 5.078894 0.0000999
chrom chrom11 chrom23 0 0.0001332 4.84e-05 2038.425 2.750074 0.4561909
chrom chrom12 chrom23 0 0.0002711 4.84e-05 2038.425 5.596499 0.0000062
chrom chrom13 chrom23 0 0.0002147 4.84e-05 2038.425 4.430895 0.0021825
chrom chrom14 chrom23 0 0.0005428 4.84e-05 2038.425 11.205324 0.0000000
chrom chrom15 chrom23 0 0.0011367 4.84e-05 2038.425 23.464421 0.0000000
chrom chrom16 chrom23 0 0.0010223 4.84e-05 2038.425 21.102187 0.0000000
chrom chrom17 chrom23 0 0.0011493 4.84e-05 2038.425 23.724210 0.0000000
chrom chrom18 chrom23 0 0.0004882 4.84e-05 2038.425 10.076293 0.0000000
chrom chrom19 chrom23 0 0.0010746 4.84e-05 2038.425 22.180865 0.0000000
chrom chrom20 chrom23 0 0.0011231 4.84e-05 2038.425 23.182437 0.0000000
chrom chrom21 chrom23 0 0.0016532 4.84e-05 2038.425 34.124483 0.0000000
chrom chrom22 chrom23 0 0.0021245 4.84e-05 2038.425 43.853271 0.0000000
# Beagle
autosomes <- df_switches %>%  filter(chrom < 23) %>% pull(Beagle)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic  p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>    <dbl>     <dbl>
1 0.000489   0.00219   0.00170      16.5 1.96e-55     1266. 0.000431  0.000547
# ℹ 2 more variables: method <chr>, alternative <chr>
# Eagle
autosomes <- df_switches %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic  p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>    <dbl>     <dbl>
1 0.000510   0.00280   0.00229      14.7 5.10e-45     1230. 0.000442  0.000579
# ℹ 2 more variables: method <chr>, alternative <chr>
# SHAPEIT
autosomes <- df_switches %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic  p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>    <dbl>     <dbl>
1 0.000592   0.00216   0.00157      20.4 1.43e-80     1295. 0.000535  0.000649
# ℹ 2 more variables: method <chr>, alternative <chr>
mod_fit <- df_switches %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)

for(i in 2:23){
  mod_fit <- df_switches %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
  
  df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pairwise <- df_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}

df_anova %>% knitr::kable()
term sumsq meansq NumDF DenDF statistic p.value chrom
method 0.0001491 0.0000746 2 1202 3681.9647 0 1
method 0.0001517 0.0000758 2 1202 4198.5629 0 2
method 0.0001322 0.0000661 2 1202 3641.1256 0 3
method 0.0001208 0.0000604 2 1202 3592.7161 0 4
method 0.0001235 0.0000618 2 1202 3082.7573 0 5
method 0.0001031 0.0000516 2 1202 2828.8144 0 6
method 0.0001377 0.0000689 2 1202 3275.4743 0 7
method 0.0001311 0.0000655 2 1202 2834.3344 0 8
method 0.0001623 0.0000811 2 1202 2145.1325 0 9
method 0.0001490 0.0000745 2 1202 3192.6028 0 10
method 0.0001437 0.0000719 2 1202 2794.6550 0 11
method 0.0001274 0.0000637 2 1202 1211.4197 0 12
method 0.0001345 0.0000672 2 1202 1955.5305 0 13
method 0.0001575 0.0000788 2 1202 2029.5949 0 14
method 0.0001894 0.0000947 2 1202 1776.8041 0 15
method 0.0002304 0.0001152 2 1202 2021.3109 0 16
method 0.0002373 0.0001187 2 1202 2081.4072 0 17
method 0.0001548 0.0000774 2 1202 1772.8476 0 18
method 0.0002054 0.0001027 2 1202 1771.9228 0 19
method 0.0002047 0.0001024 2 1202 1744.3432 0 20
method 0.0001399 0.0000700 2 1202 761.6489 0 21
method 0.0002418 0.0001209 2 1202 963.2671 0 22
method 0.0002968 0.0001484 2 1998 4651.3018 0 23
df_pairwise %>% knitr::kable()
term contrast null.value estimate std.error df statistic adj.p.value chrom
method Beagle - Eagle 0 -0.0005915 8.20e-06 1202 -72.1124435 0.0000000 1
method Beagle - SHAPEIT 0 0.0000347 8.20e-06 1202 4.2276912 0.0000753 1
method Eagle - SHAPEIT 0 0.0006262 8.20e-06 1202 76.3401347 0.0000000 1
method Beagle - Eagle 0 -0.0006033 7.70e-06 1202 -77.8881980 0.0000000 2
method Beagle - SHAPEIT 0 0.0000222 7.70e-06 1202 2.8639849 0.0118423 2
method Eagle - SHAPEIT 0 0.0006255 7.70e-06 1202 80.7521829 0.0000000 2
method Beagle - Eagle 0 -0.0005722 7.80e-06 1202 -73.6787080 0.0000000 3
method Beagle - SHAPEIT 0 0.0000035 7.80e-06 1202 0.4470285 0.8957285 3
method Eagle - SHAPEIT 0 0.0005757 7.80e-06 1202 74.1257365 0.0000000 3
method Beagle - Eagle 0 -0.0005442 7.50e-06 1202 -72.8267201 0.0000000 4
method Beagle - SHAPEIT 0 0.0000086 7.50e-06 1202 1.1535897 0.4813231 4
method Eagle - SHAPEIT 0 0.0005528 7.50e-06 1202 73.9803098 0.0000000 4
method Beagle - Eagle 0 -0.0005507 8.20e-06 1202 -67.4973130 0.0000000 5
method Beagle - SHAPEIT 0 0.0000081 8.20e-06 1202 0.9964217 0.5792582 5
method Eagle - SHAPEIT 0 0.0005588 8.20e-06 1202 68.4937347 0.0000000 5
method Beagle - Eagle 0 -0.0004977 7.80e-06 1202 -63.9557532 0.0000000 6
method Beagle - SHAPEIT 0 0.0000180 7.80e-06 1202 2.3072203 0.0551773 6
method Eagle - SHAPEIT 0 0.0005157 7.80e-06 1202 66.2629735 0.0000000 6
method Beagle - Eagle 0 -0.0005630 8.40e-06 1202 -67.3657237 0.0000000 7
method Beagle - SHAPEIT 0 0.0000432 8.40e-06 1202 5.1707846 0.0000008 7
method Eagle - SHAPEIT 0 0.0006062 8.40e-06 1202 72.5365082 0.0000000 7
method Beagle - Eagle 0 -0.0005692 8.80e-06 1202 -64.9441124 0.0000000 8
method Beagle - SHAPEIT 0 0.0000045 8.80e-06 1202 0.5157943 0.8636589 8
method Eagle - SHAPEIT 0 0.0005737 8.80e-06 1202 65.4599067 0.0000000 8
method Beagle - Eagle 0 -0.0006035 1.12e-05 1202 -53.8327217 0.0000000 9
method Beagle - SHAPEIT 0 0.0000605 1.12e-05 1202 5.3981457 0.0000002 9
method Eagle - SHAPEIT 0 0.0006640 1.12e-05 1202 59.2308674 0.0000000 9
method Beagle - Eagle 0 -0.0005858 8.80e-06 1202 -66.5288037 0.0000000 10
method Beagle - SHAPEIT 0 0.0000446 8.80e-06 1202 5.0676065 0.0000014 10
method Eagle - SHAPEIT 0 0.0006304 8.80e-06 1202 71.5964102 0.0000000 10
method Beagle - Eagle 0 -0.0005867 9.20e-06 1202 -63.4675437 0.0000000 11
method Beagle - SHAPEIT 0 0.0000230 9.20e-06 1202 2.4844345 0.0349814 11
method Eagle - SHAPEIT 0 0.0006096 9.20e-06 1202 65.9519782 0.0000000 11
method Beagle - Eagle 0 -0.0005603 1.32e-05 1202 -42.4007339 0.0000000 12
method Beagle - SHAPEIT 0 0.0000060 1.32e-05 1202 0.4505651 0.8941638 12
method Eagle - SHAPEIT 0 0.0005663 1.32e-05 1202 42.8512989 0.0000000 12
method Beagle - Eagle 0 -0.0005742 1.07e-05 1202 -53.7215046 0.0000000 13
method Beagle - SHAPEIT 0 0.0000093 1.07e-05 1202 0.8664128 0.6616136 13
method Eagle - SHAPEIT 0 0.0005834 1.07e-05 1202 54.5879174 0.0000000 13
method Beagle - Eagle 0 -0.0006249 1.14e-05 1202 -55.0367662 0.0000000 14
method Beagle - SHAPEIT 0 0.0000032 1.14e-05 1202 0.2774466 0.9584566 14
method Eagle - SHAPEIT 0 0.0006281 1.14e-05 1202 55.3142128 0.0000000 14
method Beagle - Eagle 0 -0.0006692 1.33e-05 1202 -50.2969730 0.0000000 15
method Beagle - SHAPEIT 0 0.0000341 1.33e-05 1202 2.5619267 0.0283741 15
method Eagle - SHAPEIT 0 0.0007033 1.33e-05 1202 52.8588996 0.0000000 15
method Beagle - Eagle 0 -0.0007527 1.38e-05 1202 -54.7005693 0.0000000 16
method Beagle - SHAPEIT 0 0.0000099 1.38e-05 1202 0.7184190 0.7526318 16
method Eagle - SHAPEIT 0 0.0007626 1.38e-05 1202 55.4189884 0.0000000 16
method Beagle - Eagle 0 -0.0007390 1.38e-05 1202 -53.6987663 0.0000000 17
method Beagle - SHAPEIT 0 0.0000568 1.38e-05 1202 4.1254878 0.0001170 17
method Eagle - SHAPEIT 0 0.0007958 1.38e-05 1202 57.8242541 0.0000000 17
method Beagle - Eagle 0 -0.0006146 1.20e-05 1202 -51.0276338 0.0000000 18
method Beagle - SHAPEIT 0 0.0000128 1.20e-05 1202 1.0644983 0.5363635 18
method Eagle - SHAPEIT 0 0.0006274 1.20e-05 1202 52.0921321 0.0000000 18
method Beagle - Eagle 0 -0.0006789 1.39e-05 1202 -48.9194865 0.0000000 19
method Beagle - SHAPEIT 0 0.0000682 1.39e-05 1202 4.9179190 0.0000030 19
method Eagle - SHAPEIT 0 0.0007471 1.39e-05 1202 53.8374055 0.0000000 19
method Beagle - Eagle 0 -0.0006703 1.40e-05 1202 -48.0091624 0.0000000 20
method Beagle - SHAPEIT 0 0.0000809 1.40e-05 1202 5.7923147 0.0000000 20
method Eagle - SHAPEIT 0 0.0007512 1.40e-05 1202 53.8014771 0.0000000 20
method Beagle - Eagle 0 -0.0005818 1.75e-05 1202 -33.3071614 0.0000000 21
method Beagle - SHAPEIT 0 0.0000169 1.75e-05 1202 0.9659577 0.5985721 21
method Eagle - SHAPEIT 0 0.0005987 1.75e-05 1202 34.2731192 0.0000000 21
method Beagle - Eagle 0 -0.0007039 2.04e-05 1202 -34.4670939 0.0000000 22
method Beagle - SHAPEIT 0 0.0001287 2.04e-05 1202 6.3018574 0.0000000 22
method Eagle - SHAPEIT 0 0.0008326 2.04e-05 1202 40.7689512 0.0000000 22
method Beagle - Eagle 0 -0.0005897 8.00e-06 1998 -73.8229089 0.0000000 23
method Beagle - SHAPEIT 0 0.0001345 8.00e-06 1998 16.8434174 0.0000000 23
method Eagle - SHAPEIT 0 0.0007242 8.00e-06 1998 90.6663262 0.0000000 23

Now let’s do these comparisons within each super-population:

mod_fit <- df_switches %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}

df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)

for(i in 2:23){
  mod_fit <- df_switches %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
  
  df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
  df_pop_pop <- df_pop_pop %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}

df_pop_anova %>% 
  knitr::kable()
term sumsq meansq NumDF DenDF statistic p.value chrom
method 0.0001496 0.0000748 2 1194.0000 5014.194390 0e+00 1
SUPER 0.0000119 0.0000030 4 597.0000 198.717719 0e+00 1
method:SUPER 0.0000065 0.0000008 8 1194.0000 54.685913 0e+00 1
method 0.0001496 0.0000748 2 1194.0000 5442.934800 0e+00 2
SUPER 0.0000107 0.0000027 4 597.0000 195.359641 0e+00 2
method:SUPER 0.0000053 0.0000007 8 1194.0000 48.193179 0e+00 2
method 0.0001310 0.0000655 2 1194.0000 4748.229364 0e+00 3
SUPER 0.0000103 0.0000026 4 597.0000 186.224720 0e+00 3
method:SUPER 0.0000054 0.0000007 8 1194.0000 48.543572 0e+00 3
method 0.0001206 0.0000603 2 1194.0000 4736.804165 0e+00 4
SUPER 0.0000093 0.0000023 4 597.0000 182.688205 0e+00 4
method:SUPER 0.0000050 0.0000006 8 1194.0000 49.047522 0e+00 4
method 0.0001233 0.0000616 2 1194.0000 3954.352609 0e+00 5
SUPER 0.0000112 0.0000028 4 597.0000 179.972326 0e+00 5
method:SUPER 0.0000055 0.0000007 8 1194.0000 43.907671 0e+00 5
method 0.0001032 0.0000516 2 1194.0000 3663.509419 0e+00 6
SUPER 0.0000088 0.0000022 4 597.0000 156.487220 0e+00 6
method:SUPER 0.0000051 0.0000006 8 1194.0000 45.144347 0e+00 6
method 0.0001337 0.0000668 2 1194.0000 3768.753240 0e+00 7
SUPER 0.0000115 0.0000029 4 597.0000 161.880271 0e+00 7
method:SUPER 0.0000041 0.0000005 8 1194.0000 28.879945 0e+00 7
method 0.0001302 0.0000651 2 1194.0000 3415.028099 0e+00 8
SUPER 0.0000135 0.0000034 4 597.0000 177.569924 0e+00 8
method:SUPER 0.0000050 0.0000006 8 1194.0000 33.019615 0e+00 8
method 0.0001626 0.0000813 2 1194.0000 2648.080634 0e+00 9
SUPER 0.0000224 0.0000056 4 597.0000 182.298694 0e+00 9
method:SUPER 0.0000088 0.0000011 8 1194.0000 35.873591 0e+00 9
method 0.0001466 0.0000733 2 1194.0001 3844.572265 0e+00 10
SUPER 0.0000143 0.0000036 4 596.9998 187.814753 0e+00 10
method:SUPER 0.0000053 0.0000007 8 1194.0001 34.614194 0e+00 10
method 0.0001444 0.0000722 2 1194.0000 3424.093674 0e+00 11
SUPER 0.0000146 0.0000036 4 597.0000 172.872772 0e+00 11
method:SUPER 0.0000057 0.0000007 8 1194.0000 34.027636 0e+00 11
method 0.0001250 0.0000625 2 1194.0000 1281.508285 0e+00 12
SUPER 0.0000196 0.0000049 4 597.0000 100.644592 0e+00 12
method:SUPER 0.0000049 0.0000006 8 1194.0000 12.632958 0e+00 12
method 0.0001392 0.0000696 2 1194.0000 2498.343364 0e+00 13
SUPER 0.0000207 0.0000052 4 597.0000 185.557054 0e+00 13
method:SUPER 0.0000081 0.0000010 8 1194.0000 36.167211 0e+00 13
method 0.0001579 0.0000790 2 1194.0000 2382.681969 0e+00 14
SUPER 0.0000190 0.0000047 4 597.0000 142.990364 0e+00 14
method:SUPER 0.0000071 0.0000009 8 1194.0000 26.699004 0e+00 14
method 0.0001845 0.0000923 2 1194.0000 1932.907282 0e+00 15
SUPER 0.0000278 0.0000069 4 597.0000 145.522159 0e+00 15
method:SUPER 0.0000071 0.0000009 8 1194.0000 18.509090 0e+00 15
method 0.0002177 0.0001088 2 1194.0000 2078.946898 0e+00 16
SUPER 0.0000297 0.0000074 4 597.0000 141.765615 0e+00 16
method:SUPER 0.0000060 0.0000007 8 1194.0000 14.308354 0e+00 16
method 0.0002308 0.0001154 2 1194.0000 2230.086249 0e+00 17
SUPER 0.0000338 0.0000084 4 597.0000 163.231753 0e+00 17
method:SUPER 0.0000067 0.0000008 8 1194.0000 16.297216 0e+00 17
method 0.0001554 0.0000777 2 1194.0000 2002.049963 0e+00 18
SUPER 0.0000280 0.0000070 4 597.0000 180.156650 0e+00 18
method:SUPER 0.0000061 0.0000008 8 1194.0000 19.764112 0e+00 18
method 0.0001904 0.0000952 2 1194.0000 1705.412390 0e+00 19
SUPER 0.0000361 0.0000090 4 597.0000 161.480118 0e+00 19
method:SUPER 0.0000030 0.0000004 8 1194.0000 6.764480 0e+00 19
method 0.0001931 0.0000965 2 1194.0000 1723.663367 0e+00 20
SUPER 0.0000365 0.0000091 4 597.0000 162.938879 0e+00 20
method:SUPER 0.0000037 0.0000005 8 1194.0000 8.156113 0e+00 20
method 0.0001375 0.0000687 2 1194.0000 779.869376 0e+00 21
SUPER 0.0000295 0.0000074 4 597.0000 83.703338 0e+00 21
method:SUPER 0.0000052 0.0000006 8 1194.0000 7.321987 0e+00 21
method 0.0002223 0.0001111 2 1194.0000 915.286997 0e+00 22
SUPER 0.0000468 0.0000117 4 597.0000 96.401595 0e+00 22
method:SUPER 0.0000059 0.0000007 8 1194.0000 6.071499 1e-07 22
method 0.0002968 0.0001484 2 1990.0001 6292.933267 0e+00 23
SUPER 0.0000360 0.0000090 4 994.9997 382.040973 0e+00 23
method:SUPER 0.0000168 0.0000021 8 1990.0001 89.146795 0e+00 23
df_pop_pairwise %>% knitr::kable()
SUPER term contrast null.value estimate std.error df statistic adj.p.value chrom
AFR method Beagle - Eagle 0 -0.0004848 1.22e-05 1194 -39.7886413 0.0000000 1
AFR method Beagle - SHAPEIT 0 0.0000661 1.22e-05 1194 5.4284702 0.0000002 1
AFR method Eagle - SHAPEIT 0 0.0005509 1.22e-05 1194 45.2171115 0.0000000 1
AMR method Beagle - Eagle 0 -0.0005501 1.48e-05 1194 -37.2747818 0.0000000 1
AMR method Beagle - SHAPEIT 0 0.0000178 1.48e-05 1194 1.2073952 0.4489875 1
AMR method Eagle - SHAPEIT 0 0.0005679 1.48e-05 1194 38.4821771 0.0000000 1
EAS method Beagle - Eagle 0 -0.0009117 2.04e-05 1194 -44.7834375 0.0000000 1
EAS method Beagle - SHAPEIT 0 -0.0000324 2.04e-05 1194 -1.5938996 0.2486367 1
EAS method Eagle - SHAPEIT 0 0.0008792 2.04e-05 1194 43.1895380 0.0000000 1
EUR method Beagle - Eagle 0 -0.0005309 1.67e-05 1194 -31.7907575 0.0000000 1
EUR method Beagle - SHAPEIT 0 0.0000564 1.67e-05 1194 3.3777776 0.0021759 1
EUR method Eagle - SHAPEIT 0 0.0005873 1.67e-05 1194 35.1685350 0.0000000 1
SAS method Beagle - Eagle 0 -0.0007155 1.87e-05 1194 -38.1900539 0.0000000 1
SAS method Beagle - SHAPEIT 0 0.0000169 1.87e-05 1194 0.9045021 0.6375561 1
SAS method Eagle - SHAPEIT 0 0.0007325 1.87e-05 1194 39.0945559 0.0000000 1
AFR method Beagle - Eagle 0 -0.0005135 1.17e-05 1194 -43.9081743 0.0000000 2
AFR method Beagle - SHAPEIT 0 0.0000462 1.17e-05 1194 3.9533922 0.0002405 2
AFR method Eagle - SHAPEIT 0 0.0005597 1.17e-05 1194 47.8615665 0.0000000 2
AMR method Beagle - Eagle 0 -0.0005781 1.42e-05 1194 -40.8112466 0.0000000 2
AMR method Beagle - SHAPEIT 0 0.0000021 1.42e-05 1194 0.1459337 0.9883278 2
AMR method Eagle - SHAPEIT 0 0.0005802 1.42e-05 1194 40.9571804 0.0000000 2
EAS method Beagle - Eagle 0 -0.0008646 1.95e-05 1194 -44.2511853 0.0000000 2
EAS method Beagle - SHAPEIT 0 -0.0000195 1.95e-05 1194 -0.9962264 0.5793828 2
EAS method Eagle - SHAPEIT 0 0.0008452 1.95e-05 1194 43.2549589 0.0000000 2
EUR method Beagle - Eagle 0 -0.0005174 1.60e-05 1194 -32.2778534 0.0000000 2
EUR method Beagle - SHAPEIT 0 0.0000417 1.60e-05 1194 2.5993975 0.0255885 2
EUR method Eagle - SHAPEIT 0 0.0005590 1.60e-05 1194 34.8772509 0.0000000 2
SAS method Beagle - Eagle 0 -0.0007434 1.80e-05 1194 -41.3411389 0.0000000 2
SAS method Beagle - SHAPEIT 0 0.0000085 1.80e-05 1194 0.4730133 0.8840124 2
SAS method Eagle - SHAPEIT 0 0.0007520 1.80e-05 1194 41.8141522 0.0000000 2
AFR method Beagle - Eagle 0 -0.0004931 1.17e-05 1194 -42.0962550 0.0000000 3
AFR method Beagle - SHAPEIT 0 0.0000332 1.17e-05 1194 2.8309661 0.0130887 3
AFR method Eagle - SHAPEIT 0 0.0005263 1.17e-05 1194 44.9272211 0.0000000 3
AMR method Beagle - Eagle 0 -0.0005221 1.42e-05 1194 -36.7974736 0.0000000 3
AMR method Beagle - SHAPEIT 0 -0.0000014 1.42e-05 1194 -0.0967627 0.9948513 3
AMR method Eagle - SHAPEIT 0 0.0005208 1.42e-05 1194 36.7007109 0.0000000 3
EAS method Beagle - Eagle 0 -0.0008802 1.96e-05 1194 -44.9693004 0.0000000 3
EAS method Beagle - SHAPEIT 0 -0.0000600 1.96e-05 1194 -3.0639246 0.0063175 3
EAS method Eagle - SHAPEIT 0 0.0008202 1.96e-05 1194 41.9053758 0.0000000 3
EUR method Beagle - Eagle 0 -0.0005040 1.61e-05 1194 -31.3906136 0.0000000 3
EUR method Beagle - SHAPEIT 0 0.0000200 1.61e-05 1194 1.2430270 0.4280413 3
EUR method Eagle - SHAPEIT 0 0.0005240 1.61e-05 1194 32.6336406 0.0000000 3
SAS method Beagle - Eagle 0 -0.0006650 1.80e-05 1194 -36.9150451 0.0000000 3
SAS method Beagle - SHAPEIT 0 -0.0000259 1.80e-05 1194 -1.4402671 0.3205575 3
SAS method Eagle - SHAPEIT 0 0.0006390 1.80e-05 1194 35.4747780 0.0000000 3
AFR method Beagle - Eagle 0 -0.0004339 1.13e-05 1194 -38.5466075 0.0000000 4
AFR method Beagle - SHAPEIT 0 0.0000511 1.13e-05 1194 4.5354027 0.0000189 4
AFR method Eagle - SHAPEIT 0 0.0004850 1.13e-05 1194 43.0820103 0.0000000 4
AMR method Beagle - Eagle 0 -0.0005228 1.36e-05 1194 -38.3434378 0.0000000 4
AMR method Beagle - SHAPEIT 0 -0.0000083 1.36e-05 1194 -0.6119203 0.8136340 4
AMR method Eagle - SHAPEIT 0 0.0005145 1.36e-05 1194 37.7315175 0.0000000 4
EAS method Beagle - Eagle 0 -0.0008400 1.88e-05 1194 -44.6613885 0.0000000 4
EAS method Beagle - SHAPEIT 0 -0.0000973 1.88e-05 1194 -5.1753282 0.0000008 4
EAS method Eagle - SHAPEIT 0 0.0007427 1.88e-05 1194 39.4860602 0.0000000 4
EUR method Beagle - Eagle 0 -0.0005122 1.54e-05 1194 -33.1984219 0.0000000 4
EUR method Beagle - SHAPEIT 0 0.0000316 1.54e-05 1194 2.0483651 0.1013175 4
EUR method Eagle - SHAPEIT 0 0.0005438 1.54e-05 1194 35.2467870 0.0000000 4
SAS method Beagle - Eagle 0 -0.0006292 1.73e-05 1194 -36.3475660 0.0000000 4
SAS method Beagle - SHAPEIT 0 -0.0000036 1.73e-05 1194 -0.2056646 0.9769522 4
SAS method Eagle - SHAPEIT 0 0.0006256 1.73e-05 1194 36.1419015 0.0000000 4
AFR method Beagle - Eagle 0 -0.0004639 1.25e-05 1194 -37.2522381 0.0000000 5
AFR method Beagle - SHAPEIT 0 0.0000540 1.25e-05 1194 4.3384791 0.0000462 5
AFR method Eagle - SHAPEIT 0 0.0005179 1.25e-05 1194 41.5907172 0.0000000 5
AMR method Beagle - Eagle 0 -0.0005029 1.51e-05 1194 -33.3397329 0.0000000 5
AMR method Beagle - SHAPEIT 0 -0.0000430 1.51e-05 1194 -2.8510091 0.0123197 5
AMR method Eagle - SHAPEIT 0 0.0004599 1.51e-05 1194 30.4887238 0.0000000 5
EAS method Beagle - Eagle 0 -0.0008289 2.08e-05 1194 -39.8393654 0.0000000 5
EAS method Beagle - SHAPEIT 0 -0.0000365 2.08e-05 1194 -1.7549461 0.1854418 5
EAS method Eagle - SHAPEIT 0 0.0007924 2.08e-05 1194 38.0844193 0.0000000 5
EUR method Beagle - Eagle 0 -0.0004968 1.71e-05 1194 -29.1088093 0.0000000 5
EUR method Beagle - SHAPEIT 0 0.0000271 1.71e-05 1194 1.5904161 0.2501429 5
EUR method Eagle - SHAPEIT 0 0.0005240 1.71e-05 1194 30.6992255 0.0000000 5
SAS method Beagle - Eagle 0 -0.0006651 1.91e-05 1194 -34.7312289 0.0000000 5
SAS method Beagle - SHAPEIT 0 -0.0000041 1.91e-05 1194 -0.2146232 0.9749268 5
SAS method Eagle - SHAPEIT 0 0.0006610 1.91e-05 1194 34.5166057 0.0000000 5
AFR method Beagle - Eagle 0 -0.0004307 1.18e-05 1194 -36.3778360 0.0000000 6
AFR method Beagle - SHAPEIT 0 0.0000395 1.18e-05 1194 3.3358343 0.0025230 6
AFR method Eagle - SHAPEIT 0 0.0004702 1.18e-05 1194 39.7136703 0.0000000 6
AMR method Beagle - Eagle 0 -0.0004455 1.43e-05 1194 -31.0634768 0.0000000 6
AMR method Beagle - SHAPEIT 0 -0.0000004 1.43e-05 1194 -0.0313327 0.9994589 6
AMR method Eagle - SHAPEIT 0 0.0004450 1.43e-05 1194 31.0321440 0.0000000 6
EAS method Beagle - Eagle 0 -0.0007786 1.98e-05 1194 -39.3551654 0.0000000 6
EAS method Beagle - SHAPEIT 0 -0.0000307 1.98e-05 1194 -1.5516019 0.2673213 6
EAS method Eagle - SHAPEIT 0 0.0007479 1.98e-05 1194 37.8035635 0.0000000 6
EUR method Beagle - Eagle 0 -0.0004135 1.62e-05 1194 -25.4785216 0.0000000 6
EUR method Beagle - SHAPEIT 0 0.0000458 1.62e-05 1194 2.8216635 0.0134599 6
EUR method Eagle - SHAPEIT 0 0.0004593 1.62e-05 1194 28.3001851 0.0000000 6
SAS method Beagle - Eagle 0 -0.0006084 1.82e-05 1194 -33.4147698 0.0000000 6
SAS method Beagle - SHAPEIT 0 0.0000028 1.82e-05 1194 0.1563964 0.9866059 6
SAS method Eagle - SHAPEIT 0 0.0006112 1.82e-05 1194 33.5711662 0.0000000 6
AFR method Beagle - Eagle 0 -0.0004893 1.33e-05 1194 -36.8384796 0.0000000 7
AFR method Beagle - SHAPEIT 0 0.0000892 1.33e-05 1194 6.7173393 0.0000000 7
AFR method Eagle - SHAPEIT 0 0.0005786 1.33e-05 1194 43.5558189 0.0000000 7
AMR method Beagle - Eagle 0 -0.0005097 1.61e-05 1194 -31.6815991 0.0000000 7
AMR method Beagle - SHAPEIT 0 0.0000040 1.61e-05 1194 0.2492418 0.9663358 7
AMR method Eagle - SHAPEIT 0 0.0005138 1.61e-05 1194 31.9308409 0.0000000 7
EAS method Beagle - Eagle 0 -0.0007787 2.22e-05 1194 -35.0853954 0.0000000 7
EAS method Beagle - SHAPEIT 0 -0.0000207 2.22e-05 1194 -0.9311449 0.6206665 7
EAS method Eagle - SHAPEIT 0 0.0007580 2.22e-05 1194 34.1542505 0.0000000 7
EUR method Beagle - Eagle 0 -0.0005095 1.82e-05 1194 -27.9878866 0.0000000 7
EUR method Beagle - SHAPEIT 0 0.0000678 1.82e-05 1194 3.7233301 0.0006025 7
EUR method Eagle - SHAPEIT 0 0.0005773 1.82e-05 1194 31.7112167 0.0000000 7
SAS method Beagle - Eagle 0 -0.0007076 2.04e-05 1194 -34.6411363 0.0000000 7
SAS method Beagle - SHAPEIT 0 0.0000208 2.04e-05 1194 1.0166939 0.5664368 7
SAS method Eagle - SHAPEIT 0 0.0007284 2.04e-05 1194 35.6578302 0.0000000 7
AFR method Beagle - Eagle 0 -0.0004810 1.38e-05 1194 -34.9313325 0.0000000 8
AFR method Beagle - SHAPEIT 0 0.0000378 1.38e-05 1194 2.7462505 0.0168314 8
AFR method Eagle - SHAPEIT 0 0.0005188 1.38e-05 1194 37.6775830 0.0000000 8
AMR method Beagle - Eagle 0 -0.0005401 1.67e-05 1194 -32.3807908 0.0000000 8
AMR method Beagle - SHAPEIT 0 -0.0000497 1.67e-05 1194 -2.9810694 0.0082364 8
AMR method Eagle - SHAPEIT 0 0.0004904 1.67e-05 1194 29.3997213 0.0000000 8
EAS method Beagle - Eagle 0 -0.0008343 2.30e-05 1194 -36.2603564 0.0000000 8
EAS method Beagle - SHAPEIT 0 -0.0000144 2.30e-05 1194 -0.6280035 0.8047548 8
EAS method Eagle - SHAPEIT 0 0.0008198 2.30e-05 1194 35.6323529 0.0000000 8
EUR method Beagle - Eagle 0 -0.0005210 1.89e-05 1194 -27.6024083 0.0000000 8
EUR method Beagle - SHAPEIT 0 0.0000243 1.89e-05 1194 1.2881028 0.4021488 8
EUR method Eagle - SHAPEIT 0 0.0005453 1.89e-05 1194 28.8905111 0.0000000 8
SAS method Beagle - Eagle 0 -0.0006606 2.12e-05 1194 -31.1944125 0.0000000 8
SAS method Beagle - SHAPEIT 0 0.0000044 2.12e-05 1194 0.2061953 0.9768345 8
SAS method Eagle - SHAPEIT 0 0.0006649 2.12e-05 1194 31.4006078 0.0000000 8
AFR method Beagle - Eagle 0 -0.0005045 1.75e-05 1194 -28.8649690 0.0000000 9
AFR method Beagle - SHAPEIT 0 0.0001140 1.75e-05 1194 6.5198154 0.0000000 9
AFR method Eagle - SHAPEIT 0 0.0006184 1.75e-05 1194 35.3847844 0.0000000 9
AMR method Beagle - Eagle 0 -0.0005468 2.12e-05 1194 -25.8310397 0.0000000 9
AMR method Beagle - SHAPEIT 0 0.0000109 2.12e-05 1194 0.5147044 0.8641932 9
AMR method Eagle - SHAPEIT 0 0.0005577 2.12e-05 1194 26.3457440 0.0000000 9
EAS method Beagle - Eagle 0 -0.0009980 2.92e-05 1194 -34.1746912 0.0000000 9
EAS method Beagle - SHAPEIT 0 -0.0000074 2.92e-05 1194 -0.2519426 0.9656152 9
EAS method Eagle - SHAPEIT 0 0.0009906 2.92e-05 1194 33.9227487 0.0000000 9
EUR method Beagle - Eagle 0 -0.0005329 2.40e-05 1194 -22.2458905 0.0000000 9
EUR method Beagle - SHAPEIT 0 0.0000734 2.40e-05 1194 3.0634042 0.0063281 9
EUR method Eagle - SHAPEIT 0 0.0006063 2.40e-05 1194 25.3092947 0.0000000 9
SAS method Beagle - Eagle 0 -0.0006835 2.69e-05 1194 -25.4290604 0.0000000 9
SAS method Beagle - SHAPEIT 0 0.0000554 2.69e-05 1194 2.0616579 0.0983708 9
SAS method Eagle - SHAPEIT 0 0.0007389 2.69e-05 1194 27.4907183 0.0000000 9
AFR method Beagle - Eagle 0 -0.0004960 1.38e-05 1194 -36.0113241 0.0000000 10
AFR method Beagle - SHAPEIT 0 0.0000833 1.38e-05 1194 6.0491303 0.0000000 10
AFR method Eagle - SHAPEIT 0 0.0005794 1.38e-05 1194 42.0604544 0.0000000 10
AMR method Beagle - Eagle 0 -0.0005394 1.67e-05 1194 -32.3266164 0.0000000 10
AMR method Beagle - SHAPEIT 0 0.0000218 1.67e-05 1194 1.3065352 0.3917706 10
AMR method Eagle - SHAPEIT 0 0.0005612 1.67e-05 1194 33.6331516 0.0000000 10
EAS method Beagle - Eagle 0 -0.0008549 2.30e-05 1194 -37.1449908 0.0000000 10
EAS method Beagle - SHAPEIT 0 -0.0000366 2.30e-05 1194 -1.5921365 0.2493983 10
EAS method Eagle - SHAPEIT 0 0.0008183 2.30e-05 1194 35.5528544 0.0000000 10
EUR method Beagle - Eagle 0 -0.0005128 1.89e-05 1194 -27.1635173 0.0000000 10
EUR method Beagle - SHAPEIT 0 0.0000779 1.89e-05 1194 4.1255422 0.0001171 10
EUR method Eagle - SHAPEIT 0 0.0005907 1.89e-05 1194 31.2890596 0.0000000 10
SAS method Beagle - Eagle 0 -0.0007367 2.12e-05 1194 -34.7767915 0.0000000 10
SAS method Beagle - SHAPEIT 0 0.0000168 2.12e-05 1194 0.7945323 0.7064651 10
SAS method Eagle - SHAPEIT 0 0.0007535 2.12e-05 1194 35.5713237 0.0000000 10
AFR method Beagle - Eagle 0 -0.0004786 1.45e-05 1194 -33.0405727 0.0000000 11
AFR method Beagle - SHAPEIT 0 0.0000427 1.45e-05 1194 2.9501043 0.0090788 11
AFR method Eagle - SHAPEIT 0 0.0005213 1.45e-05 1194 35.9906770 0.0000000 11
AMR method Beagle - Eagle 0 -0.0005509 1.75e-05 1194 -31.4030766 0.0000000 11
AMR method Beagle - SHAPEIT 0 -0.0000083 1.75e-05 1194 -0.4738340 0.8836342 11
AMR method Eagle - SHAPEIT 0 0.0005426 1.75e-05 1194 30.9292426 0.0000000 11
EAS method Beagle - Eagle 0 -0.0008302 2.42e-05 1194 -34.3054548 0.0000000 11
EAS method Beagle - SHAPEIT 0 -0.0000109 2.42e-05 1194 -0.4506925 0.8941073 11
EAS method Eagle - SHAPEIT 0 0.0008193 2.42e-05 1194 33.8547623 0.0000000 11
EUR method Beagle - Eagle 0 -0.0005410 1.99e-05 1194 -27.2504504 0.0000000 11
EUR method Beagle - SHAPEIT 0 0.0000536 1.99e-05 1194 2.6978328 0.0193706 11
EUR method Eagle - SHAPEIT 0 0.0005945 1.99e-05 1194 29.9482832 0.0000000 11
SAS method Beagle - Eagle 0 -0.0007511 2.23e-05 1194 -33.7229615 0.0000000 11
SAS method Beagle - SHAPEIT 0 0.0000168 2.23e-05 1194 0.7552775 0.7304877 11
SAS method Eagle - SHAPEIT 0 0.0007679 2.23e-05 1194 34.4782391 0.0000000 11
AFR method Beagle - Eagle 0 -0.0004589 2.20e-05 1194 -20.8256958 0.0000000 12
AFR method Beagle - SHAPEIT 0 0.0000635 2.20e-05 1194 2.8832788 0.0111659 12
AFR method Eagle - SHAPEIT 0 0.0005224 2.20e-05 1194 23.7089746 0.0000000 12
AMR method Beagle - Eagle 0 -0.0005511 2.67e-05 1194 -20.6483653 0.0000000 12
AMR method Beagle - SHAPEIT 0 -0.0000322 2.67e-05 1194 -1.2069318 0.4492626 12
AMR method Eagle - SHAPEIT 0 0.0005188 2.67e-05 1194 19.4414335 0.0000000 12
EAS method Beagle - Eagle 0 -0.0008548 3.68e-05 1194 -23.2202870 0.0000000 12
EAS method Beagle - SHAPEIT 0 -0.0000677 3.68e-05 1194 -1.8391891 0.1573432 12
EAS method Eagle - SHAPEIT 0 0.0007871 3.68e-05 1194 21.3810979 0.0000000 12
EUR method Beagle - Eagle 0 -0.0005199 3.02e-05 1194 -17.2168144 0.0000000 12
EUR method Beagle - SHAPEIT 0 0.0000481 3.02e-05 1194 1.5921232 0.2494040 12
EUR method Eagle - SHAPEIT 0 0.0005680 3.02e-05 1194 18.8089376 0.0000000 12
SAS method Beagle - Eagle 0 -0.0006166 3.39e-05 1194 -18.1996848 0.0000000 12
SAS method Beagle - SHAPEIT 0 -0.0000593 3.39e-05 1194 -1.7505059 0.1870160 12
SAS method Eagle - SHAPEIT 0 0.0005573 3.39e-05 1194 16.4491788 0.0000000 12
AFR method Beagle - Eagle 0 -0.0004233 1.67e-05 1194 -25.4238689 0.0000000 13
AFR method Beagle - SHAPEIT 0 0.0000487 1.67e-05 1194 2.9265783 0.0097698 13
AFR method Eagle - SHAPEIT 0 0.0004720 1.67e-05 1194 28.3504472 0.0000000 13
AMR method Beagle - Eagle 0 -0.0005647 2.02e-05 1194 -28.0014711 0.0000000 13
AMR method Beagle - SHAPEIT 0 -0.0000380 2.02e-05 1194 -1.8847916 0.1435052 13
AMR method Eagle - SHAPEIT 0 0.0005267 2.02e-05 1194 26.1166794 0.0000000 13
EAS method Beagle - Eagle 0 -0.0008419 2.78e-05 1194 -30.2609517 0.0000000 13
EAS method Beagle - SHAPEIT 0 0.0000113 2.78e-05 1194 0.4072950 0.9126339 13
EAS method Eagle - SHAPEIT 0 0.0008532 2.78e-05 1194 30.6682467 0.0000000 13
EUR method Beagle - Eagle 0 -0.0005333 2.28e-05 1194 -23.3693402 0.0000000 13
EUR method Beagle - SHAPEIT 0 0.0000316 2.28e-05 1194 1.3833907 0.3499278 13
EUR method Eagle - SHAPEIT 0 0.0005649 2.28e-05 1194 24.7527310 0.0000000 13
SAS method Beagle - Eagle 0 -0.0007708 2.56e-05 1194 -30.1039942 0.0000000 13
SAS method Beagle - SHAPEIT 0 -0.0000377 2.56e-05 1194 -1.4730930 0.3042626 13
SAS method Eagle - SHAPEIT 0 0.0007331 2.56e-05 1194 28.6309012 0.0000000 13
AFR method Beagle - Eagle 0 -0.0004913 1.82e-05 1194 -27.0560426 0.0000000 14
AFR method Beagle - SHAPEIT 0 0.0000489 1.82e-05 1194 2.6920504 0.0196953 14
AFR method Eagle - SHAPEIT 0 0.0005402 1.82e-05 1194 29.7480930 0.0000000 14
AMR method Beagle - Eagle 0 -0.0006419 2.20e-05 1194 -29.1847896 0.0000000 14
AMR method Beagle - SHAPEIT 0 -0.0000436 2.20e-05 1194 -1.9799300 0.1176013 14
AMR method Eagle - SHAPEIT 0 0.0005984 2.20e-05 1194 27.2048596 0.0000000 14
EAS method Beagle - Eagle 0 -0.0009522 3.03e-05 1194 -31.3846202 0.0000000 14
EAS method Beagle - SHAPEIT 0 -0.0000641 3.03e-05 1194 -2.1128677 0.0876476 14
EAS method Eagle - SHAPEIT 0 0.0008881 3.03e-05 1194 29.2717525 0.0000000 14
EUR method Beagle - Eagle 0 -0.0005525 2.49e-05 1194 -22.1987473 0.0000000 14
EUR method Beagle - SHAPEIT 0 0.0000416 2.49e-05 1194 1.6694587 0.2174190 14
EUR method Eagle - SHAPEIT 0 0.0005941 2.49e-05 1194 23.8682061 0.0000000 14
SAS method Beagle - Eagle 0 -0.0007275 2.79e-05 1194 -26.0506668 0.0000000 14
SAS method Beagle - SHAPEIT 0 -0.0000211 2.79e-05 1194 -0.7555807 0.7303038 14
SAS method Eagle - SHAPEIT 0 0.0007064 2.79e-05 1194 25.2950861 0.0000000 14
AFR method Beagle - Eagle 0 -0.0005743 2.18e-05 1194 -26.3535930 0.0000000 15
AFR method Beagle - SHAPEIT 0 0.0001027 2.18e-05 1194 4.7125204 0.0000082 15
AFR method Eagle - SHAPEIT 0 0.0006770 2.18e-05 1194 31.0661134 0.0000000 15
AMR method Beagle - Eagle 0 -0.0006306 2.64e-05 1194 -23.8908757 0.0000000 15
AMR method Beagle - SHAPEIT 0 -0.0000201 2.64e-05 1194 -0.7612565 0.7268558 15
AMR method Eagle - SHAPEIT 0 0.0006105 2.64e-05 1194 23.1296193 0.0000000 15
EAS method Beagle - Eagle 0 -0.0009537 3.64e-05 1194 -26.1926143 0.0000000 15
EAS method Beagle - SHAPEIT 0 -0.0000241 3.64e-05 1194 -0.6622936 0.7854026 15
EAS method Eagle - SHAPEIT 0 0.0009296 3.64e-05 1194 25.5303207 0.0000000 15
EUR method Beagle - Eagle 0 -0.0005542 2.99e-05 1194 -18.5541847 0.0000000 15
EUR method Beagle - SHAPEIT 0 0.0000871 2.99e-05 1194 2.9145756 0.0101402 15
EUR method Eagle - SHAPEIT 0 0.0006412 2.99e-05 1194 21.4687603 0.0000000 15
SAS method Beagle - Eagle 0 -0.0008598 3.35e-05 1194 -25.6579923 0.0000000 15
SAS method Beagle - SHAPEIT 0 -0.0000582 3.35e-05 1194 -1.7365068 0.1920409 15
SAS method Eagle - SHAPEIT 0 0.0008016 3.35e-05 1194 23.9214854 0.0000000 15
AFR method Beagle - Eagle 0 -0.0006647 2.28e-05 1194 -29.1210527 0.0000000 16
AFR method Beagle - SHAPEIT 0 0.0001090 2.28e-05 1194 4.7765912 0.0000060 16
AFR method Eagle - SHAPEIT 0 0.0007737 2.28e-05 1194 33.8976439 0.0000000 16
AMR method Beagle - Eagle 0 -0.0006997 2.76e-05 1194 -25.3092022 0.0000000 16
AMR method Beagle - SHAPEIT 0 -0.0000309 2.76e-05 1194 -1.1176813 0.5033142 16
AMR method Eagle - SHAPEIT 0 0.0006688 2.76e-05 1194 24.1915209 0.0000000 16
EAS method Beagle - Eagle 0 -0.0010784 3.81e-05 1194 -28.2773994 0.0000000 16
EAS method Beagle - SHAPEIT 0 -0.0000907 3.81e-05 1194 -2.3774503 0.0462395 16
EAS method Eagle - SHAPEIT 0 0.0009877 3.81e-05 1194 25.8999491 0.0000000 16
EUR method Beagle - Eagle 0 -0.0007772 3.13e-05 1194 -24.8432150 0.0000000 16
EUR method Beagle - SHAPEIT 0 -0.0000458 3.13e-05 1194 -1.4641268 0.3086647 16
EUR method Eagle - SHAPEIT 0 0.0007314 3.13e-05 1194 23.3790882 0.0000000 16
SAS method Beagle - Eagle 0 -0.0007396 3.51e-05 1194 -21.0718950 0.0000000 16
SAS method Beagle - SHAPEIT 0 -0.0000035 3.51e-05 1194 -0.1006958 0.9944255 16
SAS method Eagle - SHAPEIT 0 0.0007361 3.51e-05 1194 20.9711992 0.0000000 16
AFR method Beagle - Eagle 0 -0.0006415 2.27e-05 1194 -28.2696810 0.0000000 17
AFR method Beagle - SHAPEIT 0 0.0000717 2.27e-05 1194 3.1609305 0.0045913 17
AFR method Eagle - SHAPEIT 0 0.0007132 2.27e-05 1194 31.4306115 0.0000000 17
AMR method Beagle - Eagle 0 -0.0006918 2.75e-05 1194 -25.1708871 0.0000000 17
AMR method Beagle - SHAPEIT 0 0.0000367 2.75e-05 1194 1.3359853 0.3754574 17
AMR method Eagle - SHAPEIT 0 0.0007285 2.75e-05 1194 26.5068724 0.0000000 17
EAS method Beagle - Eagle 0 -0.0009805 3.79e-05 1194 -25.8636477 0.0000000 17
EAS method Beagle - SHAPEIT 0 -0.0000490 3.79e-05 1194 -1.2933483 0.3991825 17
EAS method Eagle - SHAPEIT 0 0.0009315 3.79e-05 1194 24.5702994 0.0000000 17
EUR method Beagle - Eagle 0 -0.0006699 3.11e-05 1194 -21.5413492 0.0000000 17
EUR method Beagle - SHAPEIT 0 0.0000758 3.11e-05 1194 2.4366683 0.0396808 17
EUR method Eagle - SHAPEIT 0 0.0007457 3.11e-05 1194 23.9780175 0.0000000 17
SAS method Beagle - Eagle 0 -0.0009283 3.49e-05 1194 -26.6049770 0.0000000 17
SAS method Beagle - SHAPEIT 0 0.0001195 3.49e-05 1194 3.4239965 0.0018447 17
SAS method Eagle - SHAPEIT 0 0.0010478 3.49e-05 1194 30.0289735 0.0000000 17
AFR method Beagle - Eagle 0 -0.0005025 1.97e-05 1194 -25.5658666 0.0000000 18
AFR method Beagle - SHAPEIT 0 0.0000428 1.97e-05 1194 2.1777036 0.0754366 18
AFR method Eagle - SHAPEIT 0 0.0005453 1.97e-05 1194 27.7435702 0.0000000 18
AMR method Beagle - Eagle 0 -0.0005614 2.38e-05 1194 -23.5813399 0.0000000 18
AMR method Beagle - SHAPEIT 0 0.0000000 2.38e-05 1194 0.0002905 1.0000000 18
AMR method Eagle - SHAPEIT 0 0.0005614 2.38e-05 1194 23.5816303 0.0000000 18
EAS method Beagle - Eagle 0 -0.0009121 3.28e-05 1194 -27.7759201 0.0000000 18
EAS method Beagle - SHAPEIT 0 -0.0000483 3.28e-05 1194 -1.4697483 0.3059004 18
EAS method Eagle - SHAPEIT 0 0.0008638 3.28e-05 1194 26.3061718 0.0000000 18
EUR method Beagle - Eagle 0 -0.0005976 2.69e-05 1194 -22.1846501 0.0000000 18
EUR method Beagle - SHAPEIT 0 0.0000092 2.69e-05 1194 0.3427056 0.9373182 18
EUR method Eagle - SHAPEIT 0 0.0006068 2.69e-05 1194 22.5273557 0.0000000 18
SAS method Beagle - Eagle 0 -0.0007351 3.02e-05 1194 -24.3222096 0.0000000 18
SAS method Beagle - SHAPEIT 0 0.0000188 3.02e-05 1194 0.6236429 0.8071752 18
SAS method Eagle - SHAPEIT 0 0.0007539 3.02e-05 1194 24.9458524 0.0000000 18
AFR method Beagle - Eagle 0 -0.0006283 2.36e-05 1194 -26.6582969 0.0000000 19
AFR method Beagle - SHAPEIT 0 0.0001134 2.36e-05 1194 4.8108655 0.0000051 19
AFR method Eagle - SHAPEIT 0 0.0007417 2.36e-05 1194 31.4691625 0.0000000 19
AMR method Beagle - Eagle 0 -0.0006456 2.85e-05 1194 -22.6150649 0.0000000 19
AMR method Beagle - SHAPEIT 0 0.0000739 2.85e-05 1194 2.5897748 0.0262807 19
AMR method Eagle - SHAPEIT 0 0.0007196 2.85e-05 1194 25.2048397 0.0000000 19
EAS method Beagle - Eagle 0 -0.0009197 3.94e-05 1194 -23.3544515 0.0000000 19
EAS method Beagle - SHAPEIT 0 -0.0000075 3.94e-05 1194 -0.1904170 0.9802099 19
EAS method Eagle - SHAPEIT 0 0.0009122 3.94e-05 1194 23.1640345 0.0000000 19
EUR method Beagle - Eagle 0 -0.0006161 3.23e-05 1194 -19.0712235 0.0000000 19
EUR method Beagle - SHAPEIT 0 0.0000805 3.23e-05 1194 2.4910241 0.0343744 19
EUR method Eagle - SHAPEIT 0 0.0006965 3.23e-05 1194 21.5622476 0.0000000 19
SAS method Beagle - Eagle 0 -0.0007272 3.62e-05 1194 -20.0648596 0.0000000 19
SAS method Beagle - SHAPEIT 0 0.0000011 3.62e-05 1194 0.0311845 0.9994640 19
SAS method Eagle - SHAPEIT 0 0.0007284 3.62e-05 1194 20.0960441 0.0000000 19
AFR method Beagle - Eagle 0 -0.0005896 2.36e-05 1194 -24.9757304 0.0000000 20
AFR method Beagle - SHAPEIT 0 0.0001246 2.36e-05 1194 5.2772216 0.0000005 20
AFR method Eagle - SHAPEIT 0 0.0007142 2.36e-05 1194 30.2529520 0.0000000 20
AMR method Beagle - Eagle 0 -0.0006870 2.86e-05 1194 -24.0269211 0.0000000 20
AMR method Beagle - SHAPEIT 0 0.0000420 2.86e-05 1194 1.4674466 0.3070305 20
AMR method Eagle - SHAPEIT 0 0.0007290 2.86e-05 1194 25.4943677 0.0000000 20
EAS method Beagle - Eagle 0 -0.0008894 3.94e-05 1194 -22.5494096 0.0000000 20
EAS method Beagle - SHAPEIT 0 0.0000280 3.94e-05 1194 0.7087858 0.7583438 20
EAS method Eagle - SHAPEIT 0 0.0009174 3.94e-05 1194 23.2581954 0.0000000 20
EUR method Beagle - Eagle 0 -0.0005743 3.24e-05 1194 -17.7501488 0.0000000 20
EUR method Beagle - SHAPEIT 0 0.0001009 3.24e-05 1194 3.1198495 0.0052617 20
EUR method Eagle - SHAPEIT 0 0.0006753 3.24e-05 1194 20.8699983 0.0000000 20
SAS method Beagle - Eagle 0 -0.0007694 3.63e-05 1194 -21.1936667 0.0000000 20
SAS method Beagle - SHAPEIT 0 0.0000598 3.63e-05 1194 1.6469038 0.2264468 20
SAS method Eagle - SHAPEIT 0 0.0008292 3.63e-05 1194 22.8405705 0.0000000 20
AFR method Beagle - Eagle 0 -0.0004929 2.96e-05 1194 -16.6421645 0.0000000 21
AFR method Beagle - SHAPEIT 0 0.0000780 2.96e-05 1194 2.6323872 0.0233345 21
AFR method Eagle - SHAPEIT 0 0.0005708 2.96e-05 1194 19.2745517 0.0000000 21
AMR method Beagle - Eagle 0 -0.0005291 3.59e-05 1194 -14.7486978 0.0000000 21
AMR method Beagle - SHAPEIT 0 -0.0000607 3.59e-05 1194 -1.6918263 0.2087106 21
AMR method Eagle - SHAPEIT 0 0.0004684 3.59e-05 1194 13.0568715 0.0000000 21
EAS method Beagle - Eagle 0 -0.0008174 4.95e-05 1194 -16.5191428 0.0000000 21
EAS method Beagle - SHAPEIT 0 0.0000127 4.95e-05 1194 0.2563844 0.9644143 21
EAS method Eagle - SHAPEIT 0 0.0008301 4.95e-05 1194 16.7755272 0.0000000 21
EUR method Beagle - Eagle 0 -0.0005720 4.06e-05 1194 -14.0914190 0.0000000 21
EUR method Beagle - SHAPEIT 0 0.0000421 4.06e-05 1194 1.0366747 0.5538347 21
EUR method Eagle - SHAPEIT 0 0.0006140 4.06e-05 1194 15.1280937 0.0000000 21
SAS method Beagle - Eagle 0 -0.0006902 4.55e-05 1194 -15.1552930 0.0000000 21
SAS method Beagle - SHAPEIT 0 -0.0000307 4.55e-05 1194 -0.6750046 0.7780931 21
SAS method Eagle - SHAPEIT 0 0.0006594 4.55e-05 1194 14.4802884 0.0000000 21
AFR method Beagle - Eagle 0 -0.0006710 3.48e-05 1194 -19.3021432 0.0000000 22
AFR method Beagle - SHAPEIT 0 0.0002068 3.48e-05 1194 5.9504723 0.0000000 22
AFR method Eagle - SHAPEIT 0 0.0008778 3.48e-05 1194 25.2526155 0.0000000 22
AMR method Beagle - Eagle 0 -0.0006841 4.21e-05 1194 -16.2486012 0.0000000 22
AMR method Beagle - SHAPEIT 0 0.0000762 4.21e-05 1194 1.8101418 0.1666555 22
AMR method Eagle - SHAPEIT 0 0.0007604 4.21e-05 1194 18.0587430 0.0000000 22
EAS method Beagle - Eagle 0 -0.0009450 5.81e-05 1194 -16.2705031 0.0000000 22
EAS method Beagle - SHAPEIT 0 0.0001413 5.81e-05 1194 2.4335804 0.0400021 22
EAS method Eagle - SHAPEIT 0 0.0010863 5.81e-05 1194 18.7040835 0.0000000 22
EUR method Beagle - Eagle 0 -0.0005896 4.76e-05 1194 -12.3746919 0.0000000 22
EUR method Beagle - SHAPEIT 0 0.0000589 4.76e-05 1194 1.2353450 0.4325231 22
EUR method Eagle - SHAPEIT 0 0.0006484 4.76e-05 1194 13.6100369 0.0000000 22
SAS method Beagle - Eagle 0 -0.0007533 5.35e-05 1194 -14.0921321 0.0000000 22
SAS method Beagle - SHAPEIT 0 0.0001057 5.35e-05 1194 1.9773718 0.1182471 22
SAS method Eagle - SHAPEIT 0 0.0008590 5.35e-05 1194 16.0695039 0.0000000 22
AFR method Beagle - Eagle 0 -0.0004678 1.54e-05 1990 -30.4654146 0.0000000 23
AFR method Beagle - SHAPEIT 0 0.0001173 1.54e-05 1990 7.6403140 0.0000000 23
AFR method Eagle - SHAPEIT 0 0.0005851 1.54e-05 1990 38.1057286 0.0000000 23
AMR method Beagle - Eagle 0 -0.0004554 1.54e-05 1990 -29.6551906 0.0000000 23
AMR method Beagle - SHAPEIT 0 0.0000767 1.54e-05 1990 4.9958668 0.0000019 23
AMR method Eagle - SHAPEIT 0 0.0005321 1.54e-05 1990 34.6510575 0.0000000 23
EAS method Beagle - Eagle 0 -0.0008262 1.54e-05 1990 -53.8035422 0.0000000 23
EAS method Beagle - SHAPEIT 0 0.0001816 1.54e-05 1990 11.8266653 0.0000000 23
EAS method Eagle - SHAPEIT 0 0.0010078 1.54e-05 1990 65.6302076 0.0000000 23
EUR method Beagle - Eagle 0 -0.0005527 1.54e-05 1990 -35.9949554 0.0000000 23
EUR method Beagle - SHAPEIT 0 0.0001158 1.54e-05 1990 7.5391191 0.0000000 23
EUR method Eagle - SHAPEIT 0 0.0006685 1.54e-05 1990 43.5340745 0.0000000 23
SAS method Beagle - Eagle 0 -0.0006463 1.54e-05 1990 -42.0871894 0.0000000 23
SAS method Beagle - SHAPEIT 0 0.0001813 1.54e-05 1990 11.8061447 0.0000000 23
SAS method Eagle - SHAPEIT 0 0.0008275 1.54e-05 1990 53.8933341 0.0000000 23
df_pop_pop %>% knitr::kable()
method term contrast null.value estimate std.error df statistic adj.p.value chrom
Beagle SUPER AFR - AMR 0 -0.0004807 0.0000669 630.7053 -7.1848755 0.0000000 1
Beagle SUPER AFR - EAS 0 -0.0018942 0.0000829 630.7053 -22.8393004 0.0000000 1
Beagle SUPER AFR - EUR 0 -0.0004813 0.0000723 630.7053 -6.6613280 0.0000000 1
Beagle SUPER AFR - SAS 0 -0.0013017 0.0000781 630.7053 -16.6613976 0.0000000 1
Beagle SUPER AMR - EAS 0 -0.0014135 0.0000879 630.7053 -16.0817395 0.0000000 1
Beagle SUPER AMR - EUR 0 -0.0000007 0.0000779 630.7053 -0.0089136 1.0000000 1
Beagle SUPER AMR - SAS 0 -0.0008210 0.0000834 630.7053 -9.8476033 0.0000000 1
Beagle SUPER EAS - EUR 0 0.0014128 0.0000920 630.7053 15.3496278 0.0000000 1
Beagle SUPER EAS - SAS 0 0.0005925 0.0000967 630.7053 6.1260957 0.0000000 1
Beagle SUPER EUR - SAS 0 -0.0008203 0.0000877 630.7053 -9.3501925 0.0000000 1
Eagle SUPER AFR - AMR 0 -0.0005460 0.0000669 630.7053 -8.1612259 0.0000000 1
Eagle SUPER AFR - EAS 0 -0.0023210 0.0000829 630.7053 -27.9865987 0.0000000 1
Eagle SUPER AFR - EUR 0 -0.0005274 0.0000723 630.7053 -7.2992369 0.0000000 1
Eagle SUPER AFR - SAS 0 -0.0015324 0.0000781 630.7053 -19.6149324 0.0000000 1
Eagle SUPER AMR - EAS 0 -0.0017751 0.0000879 630.7053 -20.1954142 0.0000000 1
Eagle SUPER AMR - EUR 0 0.0000185 0.0000779 630.7053 0.2378093 0.9992921 1
Eagle SUPER AMR - SAS 0 -0.0009864 0.0000834 630.7053 -11.8318237 0.0000000 1
Eagle SUPER EAS - EUR 0 0.0017936 0.0000920 630.7053 19.4867853 0.0000000 1
Eagle SUPER EAS - SAS 0 0.0007886 0.0000967 630.7053 8.1541414 0.0000000 1
Eagle SUPER EUR - SAS 0 -0.0010050 0.0000877 630.7053 -11.4548630 0.0000000 1
SHAPEIT SUPER AFR - AMR 0 -0.0005290 0.0000669 630.7053 -7.9071873 0.0000000 1
SHAPEIT SUPER AFR - EAS 0 -0.0019927 0.0000829 630.7053 -24.0280479 0.0000000 1
SHAPEIT SUPER AFR - EUR 0 -0.0004911 0.0000723 630.7053 -6.7960378 0.0000000 1
SHAPEIT SUPER AFR - SAS 0 -0.0013509 0.0000781 630.7053 -17.2910718 0.0000000 1
SHAPEIT SUPER AMR - EAS 0 -0.0014638 0.0000879 630.7053 -16.6536301 0.0000000 1
SHAPEIT SUPER AMR - EUR 0 0.0000379 0.0000779 630.7053 0.4864065 0.9886045 1
SHAPEIT SUPER AMR - SAS 0 -0.0008219 0.0000834 630.7053 -9.8580616 0.0000000 1
SHAPEIT SUPER EAS - EUR 0 0.0015017 0.0000920 630.7053 16.3149894 0.0000000 1
SHAPEIT SUPER EAS - SAS 0 0.0006419 0.0000967 630.7053 6.6368193 0.0000000 1
SHAPEIT SUPER EUR - SAS 0 -0.0008598 0.0000877 630.7053 -9.7999554 0.0000000 1
Beagle SUPER AFR - AMR 0 -0.0005297 0.0000643 630.6478 -8.2429775 0.0000000 2
Beagle SUPER AFR - EAS 0 -0.0018225 0.0000797 630.6478 -22.8765490 0.0000000 2
Beagle SUPER AFR - EUR 0 -0.0003888 0.0000694 630.6478 -5.6016983 0.0000003 2
Beagle SUPER AFR - SAS 0 -0.0012416 0.0000750 630.6478 -16.5441496 0.0000000 2
Beagle SUPER AMR - EAS 0 -0.0012928 0.0000844 630.6478 -15.3115428 0.0000000 2
Beagle SUPER AMR - EUR 0 0.0001409 0.0000748 630.6478 1.8825834 0.3277699 2
Beagle SUPER AMR - SAS 0 -0.0007119 0.0000801 630.6478 -8.8887089 0.0000000 2
Beagle SUPER EAS - EUR 0 0.0014337 0.0000884 630.6478 16.2150908 0.0000000 2
Beagle SUPER EAS - SAS 0 0.0005809 0.0000929 630.6478 6.2527494 0.0000000 2
Beagle SUPER EUR - SAS 0 -0.0008528 0.0000843 630.6478 -10.1185359 0.0000000 2
Eagle SUPER AFR - AMR 0 -0.0005943 0.0000643 630.6478 -9.2483756 0.0000000 2
Eagle SUPER AFR - EAS 0 -0.0021737 0.0000797 630.6478 -27.2843550 0.0000000 2
Eagle SUPER AFR - EUR 0 -0.0003927 0.0000694 630.6478 -5.6575273 0.0000002 2
Eagle SUPER AFR - SAS 0 -0.0014716 0.0000750 630.6478 -19.6083904 0.0000000 2
Eagle SUPER AMR - EAS 0 -0.0015793 0.0000844 630.6478 -18.7053518 0.0000000 2
Eagle SUPER AMR - EUR 0 0.0002016 0.0000748 630.6478 2.6941653 0.0559223 2
Eagle SUPER AMR - SAS 0 -0.0008772 0.0000801 630.6478 -10.9533597 0.0000000 2
Eagle SUPER EAS - EUR 0 0.0017810 0.0000884 630.6478 20.1429117 0.0000000 2
Eagle SUPER EAS - SAS 0 0.0007021 0.0000929 630.6478 7.5572399 0.0000000 2
Eagle SUPER EUR - SAS 0 -0.0010789 0.0000843 630.6478 -12.8012112 0.0000000 2
SHAPEIT SUPER AFR - AMR 0 -0.0005739 0.0000643 630.6478 -8.9302327 0.0000000 2
SHAPEIT SUPER AFR - EAS 0 -0.0018882 0.0000797 630.6478 -23.7012034 0.0000000 2
SHAPEIT SUPER AFR - EUR 0 -0.0003934 0.0000694 630.6478 -5.6675196 0.0000002 2
SHAPEIT SUPER AFR - SAS 0 -0.0012793 0.0000750 630.6478 -17.0468442 0.0000000 2
SHAPEIT SUPER AMR - EAS 0 -0.0013143 0.0000844 630.6478 -15.5665712 0.0000000 2
SHAPEIT SUPER AMR - EUR 0 0.0001805 0.0000748 630.6478 2.4116975 0.1134719 2
SHAPEIT SUPER AMR - SAS 0 -0.0007054 0.0000801 630.6478 -8.8083088 0.0000000 2
SHAPEIT SUPER EAS - EUR 0 0.0014948 0.0000884 630.6478 16.9064698 0.0000000 2
SHAPEIT SUPER EAS - SAS 0 0.0006089 0.0000929 630.6478 6.5538305 0.0000000 2
SHAPEIT SUPER EUR - SAS 0 -0.0008859 0.0000843 630.6478 -10.5119645 0.0000000 2
Beagle SUPER AFR - AMR 0 -0.0004770 0.0000612 634.3251 -7.7901000 0.0000000 3
Beagle SUPER AFR - EAS 0 -0.0016633 0.0000759 634.3251 -21.9124039 0.0000000 3
Beagle SUPER AFR - EUR 0 -0.0004289 0.0000661 634.3251 -6.4854370 0.0000000 3
Beagle SUPER AFR - SAS 0 -0.0011775 0.0000715 634.3251 -16.4669982 0.0000000 3
Beagle SUPER AMR - EAS 0 -0.0011863 0.0000804 634.3251 -14.7465064 0.0000000 3
Beagle SUPER AMR - EUR 0 0.0000481 0.0000713 634.3251 0.6739613 0.9619775 3
Beagle SUPER AMR - SAS 0 -0.0007005 0.0000763 634.3251 -9.1798041 0.0000000 3
Beagle SUPER EAS - EUR 0 0.0012344 0.0000842 634.3251 14.6525376 0.0000000 3
Beagle SUPER EAS - SAS 0 0.0004858 0.0000885 634.3251 5.4883007 0.0000006 3
Beagle SUPER EUR - SAS 0 -0.0007486 0.0000803 634.3251 -9.3219533 0.0000000 3
Eagle SUPER AFR - AMR 0 -0.0005060 0.0000612 634.3251 -8.2636234 0.0000000 3
Eagle SUPER AFR - EAS 0 -0.0020504 0.0000759 634.3251 -27.0112230 0.0000000 3
Eagle SUPER AFR - EUR 0 -0.0004398 0.0000661 634.3251 -6.6496732 0.0000000 3
Eagle SUPER AFR - SAS 0 -0.0013493 0.0000715 634.3251 -18.8703182 0.0000000 3
Eagle SUPER AMR - EAS 0 -0.0015444 0.0000804 634.3251 -19.1971499 0.0000000 3
Eagle SUPER AMR - EUR 0 0.0000662 0.0000713 634.3251 0.9282515 0.8859266 3
Eagle SUPER AMR - SAS 0 -0.0008434 0.0000763 634.3251 -11.0519090 0.0000000 3
Eagle SUPER EAS - EUR 0 0.0016106 0.0000842 634.3251 19.1178867 0.0000000 3
Eagle SUPER EAS - SAS 0 0.0007010 0.0000885 634.3251 7.9192358 0.0000000 3
Eagle SUPER EUR - SAS 0 -0.0009095 0.0000803 634.3251 -11.3268008 0.0000000 3
SHAPEIT SUPER AFR - AMR 0 -0.0005115 0.0000612 634.3251 -8.3541310 0.0000000 3
SHAPEIT SUPER AFR - EAS 0 -0.0017565 0.0000759 634.3251 -23.1393189 0.0000000 3
SHAPEIT SUPER AFR - EUR 0 -0.0004421 0.0000661 634.3251 -6.6851015 0.0000000 3
SHAPEIT SUPER AFR - SAS 0 -0.0012366 0.0000715 634.3251 -17.2936082 0.0000000 3
SHAPEIT SUPER AMR - EAS 0 -0.0012449 0.0000804 634.3251 -15.4748812 0.0000000 3
SHAPEIT SUPER AMR - EUR 0 0.0000694 0.0000713 634.3251 0.9731112 0.8672733 3
SHAPEIT SUPER AMR - SAS 0 -0.0007251 0.0000763 634.3251 -9.5018087 0.0000000 3
SHAPEIT SUPER EAS - EUR 0 0.0013143 0.0000842 634.3251 15.6012950 0.0000000 3
SHAPEIT SUPER EAS - SAS 0 0.0005199 0.0000885 634.3251 5.8726699 0.0000001 3
SHAPEIT SUPER EUR - SAS 0 -0.0007945 0.0000803 634.3251 -9.8935853 0.0000000 3
Beagle SUPER AFR - AMR 0 -0.0005064 0.0000560 638.4437 -9.0510630 0.0000000 4
Beagle SUPER AFR - EAS 0 -0.0014302 0.0000694 638.4437 -20.6181250 0.0000000 4
Beagle SUPER AFR - EUR 0 -0.0003830 0.0000604 638.4437 -6.3378211 0.0000000 4
Beagle SUPER AFR - SAS 0 -0.0011164 0.0000653 638.4437 -17.0851905 0.0000000 4
Beagle SUPER AMR - EAS 0 -0.0009237 0.0000735 638.4437 -12.5655292 0.0000000 4
Beagle SUPER AMR - EUR 0 0.0001234 0.0000652 638.4437 1.8937125 0.3217099 4
Beagle SUPER AMR - SAS 0 -0.0006100 0.0000697 638.4437 -8.7472869 0.0000000 4
Beagle SUPER EAS - EUR 0 0.0010471 0.0000770 638.4437 13.6022193 0.0000000 4
Beagle SUPER EAS - SAS 0 0.0003138 0.0000809 638.4437 3.8790612 0.0010923 4
Beagle SUPER EUR - SAS 0 -0.0007333 0.0000734 638.4437 -9.9940258 0.0000000 4
Eagle SUPER AFR - AMR 0 -0.0005953 0.0000560 638.4437 -10.6399188 0.0000000 4
Eagle SUPER AFR - EAS 0 -0.0018363 0.0000694 638.4437 -26.4726774 0.0000000 4
Eagle SUPER AFR - EUR 0 -0.0004613 0.0000604 638.4437 -7.6331995 0.0000000 4
Eagle SUPER AFR - SAS 0 -0.0013117 0.0000653 638.4437 -20.0737380 0.0000000 4
Eagle SUPER AMR - EAS 0 -0.0012409 0.0000735 638.4437 -16.8803516 0.0000000 4
Eagle SUPER AMR - EUR 0 0.0001340 0.0000652 638.4437 2.0565696 0.2405037 4
Eagle SUPER AMR - SAS 0 -0.0007163 0.0000697 638.4437 -10.2728393 0.0000000 4
Eagle SUPER EAS - EUR 0 0.0013749 0.0000770 638.4437 17.8604780 0.0000000 4
Eagle SUPER EAS - SAS 0 0.0005246 0.0000809 638.4437 6.4853065 0.0000000 4
Eagle SUPER EUR - SAS 0 -0.0008503 0.0000734 638.4437 -11.5883580 0.0000000 4
SHAPEIT SUPER AFR - AMR 0 -0.0005658 0.0000560 638.4437 -10.1126598 0.0000000 4
SHAPEIT SUPER AFR - EAS 0 -0.0015786 0.0000694 638.4437 -22.7574952 0.0000000 4
SHAPEIT SUPER AFR - EUR 0 -0.0004025 0.0000604 638.4437 -6.6596682 0.0000000 4
SHAPEIT SUPER AFR - SAS 0 -0.0011710 0.0000653 638.4437 -17.9210263 0.0000000 4
SHAPEIT SUPER AMR - EAS 0 -0.0010127 0.0000735 638.4437 -13.7761545 0.0000000 4
SHAPEIT SUPER AMR - EUR 0 0.0001633 0.0000652 638.4437 2.5068059 0.0903563 4
SHAPEIT SUPER AMR - SAS 0 -0.0006052 0.0000697 638.4437 -8.6786878 0.0000000 4
SHAPEIT SUPER EAS - EUR 0 0.0011761 0.0000770 638.4437 15.2772203 0.0000000 4
SHAPEIT SUPER EAS - SAS 0 0.0004076 0.0000809 638.4437 5.0384239 0.0000061 4
SHAPEIT SUPER EUR - SAS 0 -0.0007685 0.0000734 638.4437 -10.4732390 0.0000000 4
Beagle SUPER AFR - AMR 0 -0.0004595 0.0000644 635.1412 -7.1333934 0.0000000 5
Beagle SUPER AFR - EAS 0 -0.0017015 0.0000799 635.1412 -21.3077225 0.0000000 5
Beagle SUPER AFR - EUR 0 -0.0004053 0.0000696 635.1412 -5.8257167 0.0000001 5
Beagle SUPER AFR - SAS 0 -0.0012484 0.0000752 635.1412 -16.5953891 0.0000000 5
Beagle SUPER AMR - EAS 0 -0.0012420 0.0000846 635.1412 -14.6757849 0.0000000 5
Beagle SUPER AMR - EUR 0 0.0000542 0.0000750 635.1412 0.7219579 0.9514281 5
Beagle SUPER AMR - SAS 0 -0.0007889 0.0000803 635.1412 -9.8270587 0.0000000 5
Beagle SUPER EAS - EUR 0 0.0012962 0.0000886 635.1412 14.6256267 0.0000000 5
Beagle SUPER EAS - SAS 0 0.0004531 0.0000931 635.1412 4.8660624 0.0000142 5
Beagle SUPER EUR - SAS 0 -0.0008430 0.0000845 635.1412 -9.9796538 0.0000000 5
Eagle SUPER AFR - AMR 0 -0.0004985 0.0000644 635.1412 -7.7386505 0.0000000 5
Eagle SUPER AFR - EAS 0 -0.0020665 0.0000799 635.1412 -25.8787000 0.0000000 5
Eagle SUPER AFR - EUR 0 -0.0004383 0.0000696 635.1412 -6.2988992 0.0000000 5
Eagle SUPER AFR - SAS 0 -0.0014496 0.0000752 635.1412 -19.2698312 0.0000000 5
Eagle SUPER AMR - EAS 0 -0.0015681 0.0000846 635.1412 -18.5281119 0.0000000 5
Eagle SUPER AMR - EUR 0 0.0000602 0.0000750 635.1412 0.8028052 0.9297348 5
Eagle SUPER AMR - SAS 0 -0.0009511 0.0000803 635.1412 -11.8475185 0.0000000 5
Eagle SUPER EAS - EUR 0 0.0016283 0.0000886 635.1412 18.3728150 0.0000000 5
Eagle SUPER EAS - SAS 0 0.0006170 0.0000931 635.1412 6.6253528 0.0000000 5
Eagle SUPER EUR - SAS 0 -0.0010113 0.0000845 635.1412 -11.9714716 0.0000000 5
SHAPEIT SUPER AFR - AMR 0 -0.0005565 0.0000644 635.1412 -8.6396912 0.0000000 5
SHAPEIT SUPER AFR - EAS 0 -0.0017921 0.0000799 635.1412 -22.4415111 0.0000000 5
SHAPEIT SUPER AFR - EUR 0 -0.0004322 0.0000696 635.1412 -6.2120620 0.0000000 5
SHAPEIT SUPER AFR - SAS 0 -0.0013065 0.0000752 635.1412 -17.3682064 0.0000000 5
SHAPEIT SUPER AMR - EAS 0 -0.0012355 0.0000846 635.1412 -14.5991105 0.0000000 5
SHAPEIT SUPER AMR - EUR 0 0.0001243 0.0000750 635.1412 1.6571039 0.4614777 5
SHAPEIT SUPER AMR - SAS 0 -0.0007500 0.0000803 635.1412 -9.3425772 0.0000000 5
SHAPEIT SUPER EAS - EUR 0 0.0013598 0.0000886 635.1412 15.3439122 0.0000000 5
SHAPEIT SUPER EAS - SAS 0 0.0004855 0.0000931 635.1412 5.2140274 0.0000025 5
SHAPEIT SUPER EUR - SAS 0 -0.0008743 0.0000845 635.1412 -10.3496270 0.0000000 5
Beagle SUPER AFR - AMR 0 -0.0003974 0.0000584 639.1428 -6.8068381 0.0000000 6
Beagle SUPER AFR - EAS 0 -0.0014009 0.0000724 639.1428 -19.3561855 0.0000000 6
Beagle SUPER AFR - EUR 0 -0.0003120 0.0000631 639.1428 -4.9483428 0.0000095 6
Beagle SUPER AFR - SAS 0 -0.0010676 0.0000682 639.1428 -15.6596456 0.0000000 6
Beagle SUPER AMR - EAS 0 -0.0010035 0.0000767 639.1428 -13.0829367 0.0000000 6
Beagle SUPER AMR - EUR 0 0.0000853 0.0000680 639.1428 1.2553529 0.7186647 6
Beagle SUPER AMR - SAS 0 -0.0006703 0.0000728 639.1428 -9.2122375 0.0000000 6
Beagle SUPER EAS - EUR 0 0.0010888 0.0000803 639.1428 13.5560089 0.0000000 6
Beagle SUPER EAS - SAS 0 0.0003332 0.0000844 639.1428 3.9484748 0.0008292 6
Beagle SUPER EUR - SAS 0 -0.0007556 0.0000766 639.1428 -9.8690271 0.0000000 6
Eagle SUPER AFR - AMR 0 -0.0004122 0.0000584 639.1428 -7.0599745 0.0000000 6
Eagle SUPER AFR - EAS 0 -0.0017487 0.0000724 639.1428 -24.1622959 0.0000000 6
Eagle SUPER AFR - EUR 0 -0.0002948 0.0000631 639.1428 -4.6747109 0.0000353 6
Eagle SUPER AFR - SAS 0 -0.0012453 0.0000682 639.1428 -18.2656881 0.0000000 6
Eagle SUPER AMR - EAS 0 -0.0013366 0.0000767 639.1428 -17.4251325 0.0000000 6
Eagle SUPER AMR - EUR 0 0.0001174 0.0000680 639.1428 1.7265394 0.4183083 6
Eagle SUPER AMR - SAS 0 -0.0008331 0.0000728 639.1428 -11.4511457 0.0000000 6
Eagle SUPER EAS - EUR 0 0.0014539 0.0000803 639.1428 18.1013769 0.0000000 6
Eagle SUPER EAS - SAS 0 0.0005034 0.0000844 639.1428 5.9646487 0.0000000 6
Eagle SUPER EUR - SAS 0 -0.0009505 0.0000766 639.1428 -12.4150405 0.0000000 6
SHAPEIT SUPER AFR - AMR 0 -0.0004373 0.0000584 639.1428 -7.4910772 0.0000000 6
SHAPEIT SUPER AFR - EAS 0 -0.0014711 0.0000724 639.1428 -20.3260321 0.0000000 6
SHAPEIT SUPER AFR - EUR 0 -0.0003057 0.0000631 639.1428 -4.8485485 0.0000154 6
SHAPEIT SUPER AFR - SAS 0 -0.0011043 0.0000682 639.1428 -16.1971999 0.0000000 6
SHAPEIT SUPER AMR - EAS 0 -0.0010337 0.0000767 639.1428 -13.4772586 0.0000000 6
SHAPEIT SUPER AMR - EUR 0 0.0001316 0.0000680 639.1428 1.9354957 0.2995529 6
SHAPEIT SUPER AMR - SAS 0 -0.0006670 0.0000728 639.1428 -9.1669233 0.0000000 6
SHAPEIT SUPER EAS - EUR 0 0.0011653 0.0000803 639.1428 14.5082357 0.0000000 6
SHAPEIT SUPER EAS - SAS 0 0.0003668 0.0000844 639.1428 4.3459012 0.0001567 6
SHAPEIT SUPER EUR - SAS 0 -0.0007985 0.0000766 639.1428 -10.4299050 0.0000000 6
Beagle SUPER AFR - AMR 0 -0.0003883 0.0000653 639.4150 -5.9473862 0.0000000 7
Beagle SUPER AFR - EAS 0 -0.0016532 0.0000809 639.4150 -20.4228820 0.0000000 7
Beagle SUPER AFR - EUR 0 -0.0003161 0.0000705 639.4150 -4.4819484 0.0000856 7
Beagle SUPER AFR - SAS 0 -0.0011325 0.0000763 639.4150 -14.8523711 0.0000000 7
Beagle SUPER AMR - EAS 0 -0.0012648 0.0000858 639.4150 -14.7435774 0.0000000 7
Beagle SUPER AMR - EUR 0 0.0000722 0.0000760 639.4150 0.9499242 0.8771082 7
Beagle SUPER AMR - SAS 0 -0.0007442 0.0000814 639.4150 -9.1453984 0.0000000 7
Beagle SUPER EAS - EUR 0 0.0013370 0.0000898 639.4150 14.8833148 0.0000000 7
Beagle SUPER EAS - SAS 0 0.0005206 0.0000944 639.4150 5.5152983 0.0000005 7
Beagle SUPER EUR - SAS 0 -0.0008164 0.0000856 639.4150 -9.5343018 0.0000000 7
Eagle SUPER AFR - AMR 0 -0.0004087 0.0000653 639.4150 -6.2599081 0.0000000 7
Eagle SUPER AFR - EAS 0 -0.0019425 0.0000809 639.4150 -23.9975453 0.0000000 7
Eagle SUPER AFR - EUR 0 -0.0003363 0.0000705 639.4150 -4.7684742 0.0000227 7
Eagle SUPER AFR - SAS 0 -0.0013508 0.0000763 639.4150 -17.7147460 0.0000000 7
Eagle SUPER AMR - EAS 0 -0.0015338 0.0000858 639.4150 -17.8786270 0.0000000 7
Eagle SUPER AMR - EUR 0 0.0000724 0.0000760 639.4150 0.9525262 0.8760251 7
Eagle SUPER AMR - SAS 0 -0.0009421 0.0000814 639.4150 -11.5768551 0.0000000 7
Eagle SUPER EAS - EUR 0 0.0016062 0.0000898 639.4150 17.8793162 0.0000000 7
Eagle SUPER EAS - SAS 0 0.0005917 0.0000944 639.4150 6.2684207 0.0000000 7
Eagle SUPER EUR - SAS 0 -0.0010145 0.0000856 639.4150 -11.8472083 0.0000000 7
SHAPEIT SUPER AFR - AMR 0 -0.0004736 0.0000653 639.4150 -7.2525270 0.0000000 7
SHAPEIT SUPER AFR - EAS 0 -0.0017630 0.0000809 639.4150 -21.7805175 0.0000000 7
SHAPEIT SUPER AFR - EUR 0 -0.0003375 0.0000705 639.4150 -4.7859682 0.0000208 7
SHAPEIT SUPER AFR - SAS 0 -0.0012010 0.0000763 639.4150 -15.7501966 0.0000000 7
SHAPEIT SUPER AMR - EAS 0 -0.0012895 0.0000858 639.4150 -15.0312212 0.0000000 7
SHAPEIT SUPER AMR - EUR 0 0.0001360 0.0000760 639.4150 1.7886923 0.3810372 7
SHAPEIT SUPER AMR - SAS 0 -0.0007274 0.0000814 639.4150 -8.9394667 0.0000000 7
SHAPEIT SUPER EAS - EUR 0 0.0014255 0.0000898 639.4150 15.8679301 0.0000000 7
SHAPEIT SUPER EAS - SAS 0 0.0005621 0.0000944 639.4150 5.9542350 0.0000000 7
SHAPEIT SUPER EUR - SAS 0 -0.0008634 0.0000856 639.4150 -10.0833992 0.0000000 7
Beagle SUPER AFR - AMR 0 -0.0005456 0.0000651 643.0653 -8.3848693 0.0000000 8
Beagle SUPER AFR - EAS 0 -0.0017805 0.0000807 643.0653 -22.0729241 0.0000000 8
Beagle SUPER AFR - EUR 0 -0.0004309 0.0000703 643.0653 -6.1306601 0.0000000 8
Beagle SUPER AFR - SAS 0 -0.0011871 0.0000760 643.0653 -15.6221860 0.0000000 8
Beagle SUPER AMR - EAS 0 -0.0012349 0.0000855 643.0653 -14.4452760 0.0000000 8
Beagle SUPER AMR - EUR 0 0.0001147 0.0000758 643.0653 1.5137856 0.5538420 8
Beagle SUPER AMR - SAS 0 -0.0006415 0.0000811 643.0653 -7.9109164 0.0000000 8
Beagle SUPER EAS - EUR 0 0.0013496 0.0000895 643.0653 15.0757045 0.0000000 8
Beagle SUPER EAS - SAS 0 0.0005934 0.0000941 643.0653 6.3083850 0.0000000 8
Beagle SUPER EUR - SAS 0 -0.0007562 0.0000853 643.0653 -8.8618689 0.0000000 8
Eagle SUPER AFR - AMR 0 -0.0006047 0.0000651 643.0653 -9.2928435 0.0000000 8
Eagle SUPER AFR - EAS 0 -0.0021338 0.0000807 643.0653 -26.4523747 0.0000000 8
Eagle SUPER AFR - EUR 0 -0.0004708 0.0000703 643.0653 -6.6988873 0.0000000 8
Eagle SUPER AFR - SAS 0 -0.0013666 0.0000760 643.0653 -17.9850130 0.0000000 8
Eagle SUPER AMR - EAS 0 -0.0015291 0.0000855 643.0653 -17.8864814 0.0000000 8
Eagle SUPER AMR - EUR 0 0.0001338 0.0000758 643.0653 1.7664259 0.3942179 8
Eagle SUPER AMR - SAS 0 -0.0007620 0.0000811 643.0653 -9.3964716 0.0000000 8
Eagle SUPER EAS - EUR 0 0.0016630 0.0000895 643.0653 18.5756994 0.0000000 8
Eagle SUPER EAS - SAS 0 0.0007671 0.0000941 643.0653 8.1551592 0.0000000 8
Eagle SUPER EUR - SAS 0 -0.0008958 0.0000853 643.0653 -10.4979159 0.0000000 8
SHAPEIT SUPER AFR - AMR 0 -0.0006331 0.0000651 643.0653 -9.7302632 0.0000000 8
SHAPEIT SUPER AFR - EAS 0 -0.0018328 0.0000807 643.0653 -22.7208813 0.0000000 8
SHAPEIT SUPER AFR - EUR 0 -0.0004444 0.0000703 643.0653 -6.3228291 0.0000000 8
SHAPEIT SUPER AFR - SAS 0 -0.0012205 0.0000760 643.0653 -16.0624092 0.0000000 8
SHAPEIT SUPER AMR - EAS 0 -0.0011996 0.0000855 643.0653 -14.0326569 0.0000000 8
SHAPEIT SUPER AMR - EUR 0 0.0001887 0.0000758 643.0653 2.4908690 0.0939318 8
SHAPEIT SUPER AMR - SAS 0 -0.0005874 0.0000811 643.0653 -7.2438832 0.0000000 8
SHAPEIT SUPER EAS - EUR 0 0.0013884 0.0000895 643.0653 15.5086769 0.0000000 8
SHAPEIT SUPER EAS - SAS 0 0.0006122 0.0000941 643.0653 6.5084093 0.0000000 8
SHAPEIT SUPER EUR - SAS 0 -0.0007762 0.0000853 643.0653 -9.0956031 0.0000000 8
Beagle SUPER AFR - AMR 0 -0.0003911 0.0000759 652.0586 -5.1557551 0.0000033 9
Beagle SUPER AFR - EAS 0 -0.0020236 0.0000941 652.0586 -21.5162240 0.0000000 9
Beagle SUPER AFR - EUR 0 -0.0005123 0.0000819 652.0586 -6.2518878 0.0000000 9
Beagle SUPER AFR - SAS 0 -0.0013780 0.0000886 652.0586 -15.5537726 0.0000000 9
Beagle SUPER AMR - EAS 0 -0.0016325 0.0000997 652.0586 -16.3777400 0.0000000 9
Beagle SUPER AMR - EUR 0 -0.0001212 0.0000883 652.0586 -1.3716019 0.6461377 9
Beagle SUPER AMR - SAS 0 -0.0009869 0.0000945 652.0586 -10.4378640 0.0000000 9
Beagle SUPER EAS - EUR 0 0.0015113 0.0001044 652.0586 14.4789160 0.0000000 9
Beagle SUPER EAS - SAS 0 0.0006456 0.0001097 652.0586 5.8862691 0.0000001 9
Beagle SUPER EUR - SAS 0 -0.0008657 0.0000995 652.0586 -8.7011001 0.0000000 9
Eagle SUPER AFR - AMR 0 -0.0004335 0.0000759 652.0586 -5.7140026 0.0000002 9
Eagle SUPER AFR - EAS 0 -0.0025171 0.0000941 652.0586 -26.7632832 0.0000000 9
Eagle SUPER AFR - EUR 0 -0.0005407 0.0000819 652.0586 -6.5984590 0.0000000 9
Eagle SUPER AFR - SAS 0 -0.0015570 0.0000886 652.0586 -17.5736207 0.0000000 9
Eagle SUPER AMR - EAS 0 -0.0020836 0.0000997 652.0586 -20.9037721 0.0000000 9
Eagle SUPER AMR - EUR 0 -0.0001072 0.0000883 652.0586 -1.2136834 0.7434499 9
Eagle SUPER AMR - SAS 0 -0.0011235 0.0000945 652.0586 -11.8826488 0.0000000 9
Eagle SUPER EAS - EUR 0 0.0019764 0.0001044 652.0586 18.9346882 0.0000000 9
Eagle SUPER EAS - SAS 0 0.0009601 0.0001097 652.0586 8.7540894 0.0000000 9
Eagle SUPER EUR - SAS 0 -0.0010163 0.0000995 652.0586 -10.2142941 0.0000000 9
SHAPEIT SUPER AFR - AMR 0 -0.0004942 0.0000759 652.0586 -6.5141598 0.0000000 9
SHAPEIT SUPER AFR - EAS 0 -0.0021449 0.0000941 652.0586 -22.8060605 0.0000000 9
SHAPEIT SUPER AFR - EUR 0 -0.0005529 0.0000819 652.0586 -6.7469542 0.0000000 9
SHAPEIT SUPER AFR - SAS 0 -0.0014366 0.0000886 652.0586 -16.2145361 0.0000000 9
SHAPEIT SUPER AMR - EAS 0 -0.0016507 0.0000997 652.0586 -16.5608711 0.0000000 9
SHAPEIT SUPER AMR - EUR 0 -0.0000587 0.0000883 652.0586 -0.6643017 0.9639017 9
SHAPEIT SUPER AMR - SAS 0 -0.0009424 0.0000945 652.0586 -9.9670512 0.0000000 9
SHAPEIT SUPER EAS - EUR 0 0.0015920 0.0001044 652.0586 15.2524531 0.0000000 9
SHAPEIT SUPER EAS - SAS 0 0.0007084 0.0001097 652.0586 6.4585646 0.0000000 9
SHAPEIT SUPER EUR - SAS 0 -0.0008837 0.0000995 652.0586 -8.8817444 0.0000000 9
Beagle SUPER AFR - AMR 0 -0.0004560 0.0000632 646.0101 -7.2155670 0.0000000 10
Beagle SUPER AFR - EAS 0 -0.0016612 0.0000783 646.0101 -21.2058333 0.0000000 10
Beagle SUPER AFR - EUR 0 -0.0003958 0.0000683 646.0101 -5.7992752 0.0000001 10
Beagle SUPER AFR - SAS 0 -0.0012602 0.0000738 646.0101 -17.0771050 0.0000000 10
Beagle SUPER AMR - EAS 0 -0.0012053 0.0000830 646.0101 -14.5171021 0.0000000 10
Beagle SUPER AMR - EUR 0 0.0000601 0.0000736 646.0101 0.8170491 0.9253880 10
Beagle SUPER AMR - SAS 0 -0.0008043 0.0000788 646.0101 -10.2125204 0.0000000 10
Beagle SUPER EAS - EUR 0 0.0012654 0.0000869 646.0101 14.5545783 0.0000000 10
Beagle SUPER EAS - SAS 0 0.0004010 0.0000914 646.0101 4.3895627 0.0001291 10
Beagle SUPER EUR - SAS 0 -0.0008644 0.0000829 646.0101 -10.4303925 0.0000000 10
Eagle SUPER AFR - AMR 0 -0.0004993 0.0000632 646.0101 -7.9010580 0.0000000 10
Eagle SUPER AFR - EAS 0 -0.0020201 0.0000783 646.0101 -25.7866915 0.0000000 10
Eagle SUPER AFR - EUR 0 -0.0004126 0.0000683 646.0101 -6.0452018 0.0000000 10
Eagle SUPER AFR - SAS 0 -0.0015008 0.0000738 646.0101 -20.3375258 0.0000000 10
Eagle SUPER AMR - EAS 0 -0.0015208 0.0000830 646.0101 -18.3176845 0.0000000 10
Eagle SUPER AMR - EUR 0 0.0000867 0.0000736 646.0101 1.1775897 0.7642543 10
Eagle SUPER AMR - SAS 0 -0.0010015 0.0000788 646.0101 -12.7176990 0.0000000 10
Eagle SUPER EAS - EUR 0 0.0016075 0.0000869 646.0101 18.4890851 0.0000000 10
Eagle SUPER EAS - SAS 0 0.0005193 0.0000914 646.0101 5.6839751 0.0000002 10
Eagle SUPER EUR - SAS 0 -0.0010882 0.0000829 646.0101 -13.1311916 0.0000000 10
SHAPEIT SUPER AFR - AMR 0 -0.0005175 0.0000632 646.0101 -8.1892208 0.0000000 10
SHAPEIT SUPER AFR - EAS 0 -0.0017812 0.0000783 646.0101 -22.7372628 0.0000000 10
SHAPEIT SUPER AFR - EUR 0 -0.0004013 0.0000683 646.0101 -5.8789343 0.0000001 10
SHAPEIT SUPER AFR - SAS 0 -0.0013267 0.0000738 646.0101 -17.9781811 0.0000000 10
SHAPEIT SUPER AMR - EAS 0 -0.0012637 0.0000830 646.0101 -15.2210328 0.0000000 10
SHAPEIT SUPER AMR - EUR 0 0.0001162 0.0000736 646.0101 1.5792674 0.5112671 10
SHAPEIT SUPER AMR - SAS 0 -0.0008092 0.0000788 646.0101 -10.2756213 0.0000000 10
SHAPEIT SUPER EAS - EUR 0 0.0013799 0.0000869 646.0101 15.8719329 0.0000000 10
SHAPEIT SUPER EAS - SAS 0 0.0004545 0.0000914 646.0101 4.9749049 0.0000083 10
SHAPEIT SUPER EUR - SAS 0 -0.0009254 0.0000829 646.0101 -11.1671763 0.0000000 10
Beagle SUPER AFR - AMR 0 -0.0005333 0.0000673 644.6732 -7.9205795 0.0000000 11
Beagle SUPER AFR - EAS 0 -0.0017392 0.0000835 644.6732 -20.8383111 0.0000000 11
Beagle SUPER AFR - EUR 0 -0.0004278 0.0000727 644.6732 -5.8826704 0.0000001 11
Beagle SUPER AFR - SAS 0 -0.0012997 0.0000786 644.6732 -16.5309460 0.0000000 11
Beagle SUPER AMR - EAS 0 -0.0012060 0.0000885 644.6732 -13.6337227 0.0000000 11
Beagle SUPER AMR - EUR 0 0.0001055 0.0000784 644.6732 1.3451111 0.6630158 11
Beagle SUPER AMR - SAS 0 -0.0007665 0.0000839 644.6732 -9.1350299 0.0000000 11
Beagle SUPER EAS - EUR 0 0.0013114 0.0000926 644.6732 14.1579502 0.0000000 11
Beagle SUPER EAS - SAS 0 0.0004395 0.0000973 644.6732 4.5155908 0.0000734 11
Beagle SUPER EUR - SAS 0 -0.0008719 0.0000883 644.6732 -9.8753590 0.0000000 11
Eagle SUPER AFR - AMR 0 -0.0006056 0.0000673 644.6732 -8.9955370 0.0000000 11
Eagle SUPER AFR - EAS 0 -0.0020909 0.0000835 644.6732 -25.0513804 0.0000000 11
Eagle SUPER AFR - EUR 0 -0.0004902 0.0000727 644.6732 -6.7407832 0.0000000 11
Eagle SUPER AFR - SAS 0 -0.0015723 0.0000786 644.6732 -19.9973909 0.0000000 11
Eagle SUPER AMR - EAS 0 -0.0014852 0.0000885 644.6732 -16.7908425 0.0000000 11
Eagle SUPER AMR - EUR 0 0.0001154 0.0000784 644.6732 1.4722585 0.5809442 11
Eagle SUPER AMR - SAS 0 -0.0009666 0.0000839 644.6732 -11.5207565 0.0000000 11
Eagle SUPER EAS - EUR 0 0.0016007 0.0000926 644.6732 17.2804423 0.0000000 11
Eagle SUPER EAS - SAS 0 0.0005186 0.0000973 644.6732 5.3281924 0.0000014 11
Eagle SUPER EUR - SAS 0 -0.0010821 0.0000883 644.6732 -12.2553998 0.0000000 11
SHAPEIT SUPER AFR - AMR 0 -0.0005843 0.0000673 644.6732 -8.6787111 0.0000000 11
SHAPEIT SUPER AFR - EAS 0 -0.0017929 0.0000835 644.6732 -21.4809339 0.0000000 11
SHAPEIT SUPER AFR - EUR 0 -0.0004170 0.0000727 644.6732 -5.7337916 0.0000002 11
SHAPEIT SUPER AFR - SAS 0 -0.0013256 0.0000786 644.6732 -16.8604480 0.0000000 11
SHAPEIT SUPER AMR - EAS 0 -0.0012086 0.0000885 644.6732 -13.6630476 0.0000000 11
SHAPEIT SUPER AMR - EUR 0 0.0001673 0.0000784 644.6732 2.1342368 0.2068323 11
SHAPEIT SUPER AMR - SAS 0 -0.0007413 0.0000839 644.6732 -8.8354659 0.0000000 11
SHAPEIT SUPER EAS - EUR 0 0.0013759 0.0000926 644.6732 14.8538678 0.0000000 11
SHAPEIT SUPER EAS - SAS 0 0.0004672 0.0000973 644.6732 4.8004807 0.0000194 11
SHAPEIT SUPER EUR - SAS 0 -0.0009087 0.0000883 644.6732 -10.2913976 0.0000000 11
Beagle SUPER AFR - AMR 0 -0.0004762 0.0000951 652.7626 -5.0094721 0.0000070 12
Beagle SUPER AFR - EAS 0 -0.0017950 0.0001179 652.7626 -15.2314551 0.0000000 12
Beagle SUPER AFR - EUR 0 -0.0004501 0.0001027 652.7626 -4.3837139 0.0001322 12
Beagle SUPER AFR - SAS 0 -0.0014503 0.0001110 652.7626 -13.0638189 0.0000000 12
Beagle SUPER AMR - EAS 0 -0.0013188 0.0001249 652.7626 -10.5590101 0.0000000 12
Beagle SUPER AMR - EUR 0 0.0000261 0.0001107 652.7626 0.2356264 0.9993175 12
Beagle SUPER AMR - SAS 0 -0.0009741 0.0001185 652.7626 -8.2219988 0.0000000 12
Beagle SUPER EAS - EUR 0 0.0013449 0.0001308 652.7626 10.2827046 0.0000000 12
Beagle SUPER EAS - SAS 0 0.0003447 0.0001374 652.7626 2.5083439 0.0899880 12
Beagle SUPER EUR - SAS 0 -0.0010002 0.0001247 652.7626 -8.0225338 0.0000000 12
Eagle SUPER AFR - AMR 0 -0.0005684 0.0000951 652.7626 -5.9793994 0.0000000 12
Eagle SUPER AFR - EAS 0 -0.0021910 0.0001179 652.7626 -18.5913293 0.0000000 12
Eagle SUPER AFR - EUR 0 -0.0005112 0.0001027 652.7626 -4.9783823 0.0000081 12
Eagle SUPER AFR - SAS 0 -0.0016081 0.0001110 652.7626 -14.4850317 0.0000000 12
Eagle SUPER AMR - EAS 0 -0.0016226 0.0001249 652.7626 -12.9910281 0.0000000 12
Eagle SUPER AMR - EUR 0 0.0000572 0.0001107 652.7626 0.5169419 0.9856670 12
Eagle SUPER AMR - SAS 0 -0.0010397 0.0001185 652.7626 -8.7754908 0.0000000 12
Eagle SUPER EAS - EUR 0 0.0016798 0.0001308 652.7626 12.8432520 0.0000000 12
Eagle SUPER EAS - SAS 0 0.0005829 0.0001374 652.7626 4.2414451 0.0002456 12
Eagle SUPER EUR - SAS 0 -0.0010969 0.0001247 652.7626 -8.7983103 0.0000000 12
SHAPEIT SUPER AFR - AMR 0 -0.0005720 0.0000951 652.7626 -6.0165577 0.0000000 12
SHAPEIT SUPER AFR - EAS 0 -0.0019263 0.0001179 652.7626 -16.3450149 0.0000000 12
SHAPEIT SUPER AFR - EUR 0 -0.0004656 0.0001027 652.7626 -4.5341582 0.0000673 12
SHAPEIT SUPER AFR - SAS 0 -0.0015731 0.0001110 652.7626 -14.1702843 0.0000000 12
SHAPEIT SUPER AMR - EAS 0 -0.0013543 0.0001249 652.7626 -10.8432093 0.0000000 12
SHAPEIT SUPER AMR - EUR 0 0.0001064 0.0001107 652.7626 0.9608960 0.8725082 12
SHAPEIT SUPER AMR - SAS 0 -0.0010012 0.0001185 652.7626 -8.4507366 0.0000000 12
SHAPEIT SUPER EAS - EUR 0 0.0014607 0.0001308 652.7626 11.1679654 0.0000000 12
SHAPEIT SUPER EAS - SAS 0 0.0003531 0.0001374 652.7626 2.5694430 0.0772887 12
SHAPEIT SUPER EUR - SAS 0 -0.0011076 0.0001247 652.7626 -8.8839123 0.0000000 12
Beagle SUPER AFR - AMR 0 -0.0003963 0.0000674 660.9148 -5.8836425 0.0000001 13
Beagle SUPER AFR - EAS 0 -0.0018096 0.0000835 660.9148 -21.6699623 0.0000000 13
Beagle SUPER AFR - EUR 0 -0.0004075 0.0000728 660.9148 -5.6000461 0.0000003 13
Beagle SUPER AFR - SAS 0 -0.0012242 0.0000787 660.9148 -15.5626801 0.0000000 13
Beagle SUPER AMR - EAS 0 -0.0014133 0.0000885 660.9148 -15.9687917 0.0000000 13
Beagle SUPER AMR - EUR 0 -0.0000111 0.0000784 660.9148 -0.1419189 0.9999087 13
Beagle SUPER AMR - SAS 0 -0.0008279 0.0000839 660.9148 -9.8621509 0.0000000 13
Beagle SUPER EAS - EUR 0 0.0014021 0.0000927 660.9148 15.1291935 0.0000000 13
Beagle SUPER EAS - SAS 0 0.0005854 0.0000974 660.9148 6.0109070 0.0000000 13
Beagle SUPER EUR - SAS 0 -0.0008168 0.0000883 660.9148 -9.2459135 0.0000000 13
Eagle SUPER AFR - AMR 0 -0.0005377 0.0000674 660.9148 -7.9830149 0.0000000 13
Eagle SUPER AFR - EAS 0 -0.0022281 0.0000835 660.9148 -26.6819860 0.0000000 13
Eagle SUPER AFR - EUR 0 -0.0005174 0.0000728 660.9148 -7.1117186 0.0000000 13
Eagle SUPER AFR - SAS 0 -0.0015717 0.0000787 660.9148 -19.9798086 0.0000000 13
Eagle SUPER AMR - EAS 0 -0.0016904 0.0000885 660.9148 -19.1000713 0.0000000 13
Eagle SUPER AMR - EUR 0 0.0000203 0.0000784 660.9148 0.2587087 0.9990134 13
Eagle SUPER AMR - SAS 0 -0.0010340 0.0000839 660.9148 -12.3167330 0.0000000 13
Eagle SUPER EAS - EUR 0 0.0017107 0.0000927 660.9148 18.4584827 0.0000000 13
Eagle SUPER EAS - SAS 0 0.0006564 0.0000974 660.9148 6.7406680 0.0000000 13
Eagle SUPER EUR - SAS 0 -0.0010543 0.0000883 660.9148 -11.9342267 0.0000000 13
SHAPEIT SUPER AFR - AMR 0 -0.0004831 0.0000674 660.9148 -7.1713507 0.0000000 13
SHAPEIT SUPER AFR - EAS 0 -0.0018470 0.0000835 660.9148 -22.1178004 0.0000000 13
SHAPEIT SUPER AFR - EUR 0 -0.0004246 0.0000728 660.9148 -5.8358708 0.0000001 13
SHAPEIT SUPER AFR - SAS 0 -0.0013107 0.0000787 660.9148 -16.6615922 0.0000000 13
SHAPEIT SUPER AMR - EAS 0 -0.0013639 0.0000885 660.9148 -15.4112535 0.0000000 13
SHAPEIT SUPER AMR - EUR 0 0.0000584 0.0000784 660.9148 0.7451345 0.9457257 13
SHAPEIT SUPER AMR - SAS 0 -0.0008276 0.0000839 660.9148 -9.8586381 0.0000000 13
SHAPEIT SUPER EAS - EUR 0 0.0014224 0.0000927 660.9148 15.3475752 0.0000000 13
SHAPEIT SUPER EAS - SAS 0 0.0005363 0.0000974 660.9148 5.5072397 0.0000005 13
SHAPEIT SUPER EUR - SAS 0 -0.0008861 0.0000883 660.9148 -10.0302434 0.0000000 13
Beagle SUPER AFR - AMR 0 -0.0005153 0.0000781 653.1927 -6.6005741 0.0000000 14
Beagle SUPER AFR - EAS 0 -0.0018119 0.0000968 653.1927 -18.7223894 0.0000000 14
Beagle SUPER AFR - EUR 0 -0.0004380 0.0000843 653.1927 -5.1944788 0.0000027 14
Beagle SUPER AFR - SAS 0 -0.0013179 0.0000912 653.1927 -14.4556755 0.0000000 14
Beagle SUPER AMR - EAS 0 -0.0012966 0.0001026 653.1927 -12.6419026 0.0000000 14
Beagle SUPER AMR - EUR 0 0.0000773 0.0000909 653.1927 0.8499212 0.9147422 14
Beagle SUPER AMR - SAS 0 -0.0008026 0.0000973 653.1927 -8.2495488 0.0000000 14
Beagle SUPER EAS - EUR 0 0.0013739 0.0001074 653.1927 12.7916893 0.0000000 14
Beagle SUPER EAS - SAS 0 0.0004940 0.0001129 653.1927 4.3775452 0.0001359 14
Beagle SUPER EUR - SAS 0 -0.0008799 0.0001024 653.1927 -8.5941837 0.0000000 14
Eagle SUPER AFR - AMR 0 -0.0006659 0.0000781 653.1927 -8.5299660 0.0000000 14
Eagle SUPER AFR - EAS 0 -0.0022729 0.0000968 653.1927 -23.4850665 0.0000000 14
Eagle SUPER AFR - EUR 0 -0.0004992 0.0000843 653.1927 -5.9200570 0.0000001 14
Eagle SUPER AFR - SAS 0 -0.0015540 0.0000912 653.1927 -17.0458377 0.0000000 14
Eagle SUPER AMR - EAS 0 -0.0016070 0.0001026 653.1927 -15.6672839 0.0000000 14
Eagle SUPER AMR - EUR 0 0.0001667 0.0000909 653.1927 1.8337321 0.3549676 14
Eagle SUPER AMR - SAS 0 -0.0008881 0.0000973 653.1927 -9.1285414 0.0000000 14
Eagle SUPER EAS - EUR 0 0.0017737 0.0001074 653.1927 16.5134563 0.0000000 14
Eagle SUPER EAS - SAS 0 0.0007188 0.0001129 653.1927 6.3693024 0.0000000 14
Eagle SUPER EUR - SAS 0 -0.0010548 0.0001024 653.1927 -10.3030689 0.0000000 14
SHAPEIT SUPER AFR - AMR 0 -0.0006077 0.0000781 653.1927 -7.7846457 0.0000000 14
SHAPEIT SUPER AFR - EAS 0 -0.0019249 0.0000968 653.1927 -19.8899273 0.0000000 14
SHAPEIT SUPER AFR - EUR 0 -0.0004454 0.0000843 653.1927 -5.2814633 0.0000017 14
SHAPEIT SUPER AFR - SAS 0 -0.0013879 0.0000912 653.1927 -15.2233350 0.0000000 14
SHAPEIT SUPER AMR - EAS 0 -0.0013172 0.0001026 653.1927 -12.8423257 0.0000000 14
SHAPEIT SUPER AMR - EUR 0 0.0001624 0.0000909 653.1927 1.7860371 0.3825800 14
SHAPEIT SUPER AMR - SAS 0 -0.0007802 0.0000973 653.1927 -8.0187899 0.0000000 14
SHAPEIT SUPER EAS - EUR 0 0.0014796 0.0001074 653.1927 13.7754085 0.0000000 14
SHAPEIT SUPER EAS - SAS 0 0.0005371 0.0001129 653.1927 4.7586174 0.0000236 14
SHAPEIT SUPER EUR - SAS 0 -0.0009425 0.0001024 653.1927 -9.2061288 0.0000000 14
Beagle SUPER AFR - AMR 0 -0.0004353 0.0000914 656.1872 -4.7618899 0.0000233 15
Beagle SUPER AFR - EAS 0 -0.0021699 0.0001133 656.1872 -19.1473359 0.0000000 15
Beagle SUPER AFR - EUR 0 -0.0006028 0.0000987 656.1872 -6.1052685 0.0000000 15
Beagle SUPER AFR - SAS 0 -0.0015207 0.0001068 656.1872 -14.2444128 0.0000000 15
Beagle SUPER AMR - EAS 0 -0.0017346 0.0001201 656.1872 -14.4423262 0.0000000 15
Beagle SUPER AMR - EUR 0 -0.0001675 0.0001065 656.1872 -1.5738279 0.5147790 15
Beagle SUPER AMR - SAS 0 -0.0010854 0.0001139 656.1872 -9.5269507 0.0000000 15
Beagle SUPER EAS - EUR 0 0.0015670 0.0001258 656.1872 12.4595392 0.0000000 15
Beagle SUPER EAS - SAS 0 0.0006492 0.0001322 656.1872 4.9126013 0.0000112 15
Beagle SUPER EUR - SAS 0 -0.0009178 0.0001199 656.1872 -7.6558970 0.0000000 15
Eagle SUPER AFR - AMR 0 -0.0004916 0.0000914 656.1872 -5.3780183 0.0000010 15
Eagle SUPER AFR - EAS 0 -0.0025493 0.0001133 656.1872 -22.4952292 0.0000000 15
Eagle SUPER AFR - EUR 0 -0.0005827 0.0000987 656.1872 -5.9014491 0.0000001 15
Eagle SUPER AFR - SAS 0 -0.0018062 0.0001068 656.1872 -16.9190560 0.0000000 15
Eagle SUPER AMR - EAS 0 -0.0020577 0.0001201 656.1872 -17.1323231 0.0000000 15
Eagle SUPER AMR - EUR 0 -0.0000911 0.0001065 656.1872 -0.8556841 0.9127880 15
Eagle SUPER AMR - SAS 0 -0.0013146 0.0001139 656.1872 -11.5388757 0.0000000 15
Eagle SUPER EAS - EUR 0 0.0019666 0.0001258 656.1872 15.6361726 0.0000000 15
Eagle SUPER EAS - SAS 0 0.0007431 0.0001322 656.1872 5.6229133 0.0000003 15
Eagle SUPER EUR - SAS 0 -0.0012235 0.0001199 656.1872 -10.2054981 0.0000000 15
SHAPEIT SUPER AFR - AMR 0 -0.0005581 0.0000914 656.1872 -6.1051462 0.0000000 15
SHAPEIT SUPER AFR - EAS 0 -0.0022967 0.0001133 656.1872 -20.2663472 0.0000000 15
SHAPEIT SUPER AFR - EUR 0 -0.0006185 0.0000987 656.1872 -6.2636999 0.0000000 15
SHAPEIT SUPER AFR - SAS 0 -0.0016815 0.0001068 656.1872 -15.7515208 0.0000000 15
SHAPEIT SUPER AMR - EAS 0 -0.0017386 0.0001201 656.1872 -14.4758028 0.0000000 15
SHAPEIT SUPER AMR - EUR 0 -0.0000604 0.0001065 656.1872 -0.5672865 0.9797282 15
SHAPEIT SUPER AMR - SAS 0 -0.0011234 0.0001139 656.1872 -9.8613710 0.0000000 15
SHAPEIT SUPER EAS - EUR 0 0.0016782 0.0001258 656.1872 13.3434417 0.0000000 15
SHAPEIT SUPER EAS - SAS 0 0.0006151 0.0001322 656.1872 4.6547380 0.0000386 15
SHAPEIT SUPER EUR - SAS 0 -0.0010631 0.0001199 656.1872 -8.8674629 0.0000000 15
Beagle SUPER AFR - AMR 0 -0.0006495 0.0000979 653.4378 -6.6332752 0.0000000 16
Beagle SUPER AFR - EAS 0 -0.0023399 0.0001214 653.4378 -19.2755192 0.0000000 16
Beagle SUPER AFR - EUR 0 -0.0005213 0.0001058 653.4378 -4.9284923 0.0000104 16
Beagle SUPER AFR - SAS 0 -0.0016488 0.0001144 653.4378 -14.4187146 0.0000000 16
Beagle SUPER AMR - EAS 0 -0.0016904 0.0001287 653.4378 -13.1389254 0.0000000 16
Beagle SUPER AMR - EUR 0 0.0001283 0.0001140 653.4378 1.1247215 0.7934607 16
Beagle SUPER AMR - SAS 0 -0.0009993 0.0001220 653.4378 -8.1886747 0.0000000 16
Beagle SUPER EAS - EUR 0 0.0018186 0.0001347 653.4378 13.4989089 0.0000000 16
Beagle SUPER EAS - SAS 0 0.0006911 0.0001416 653.4378 4.8817205 0.0000131 16
Beagle SUPER EUR - SAS 0 -0.0011276 0.0001284 653.4378 -8.7803472 0.0000000 16
Eagle SUPER AFR - AMR 0 -0.0006846 0.0000979 653.4378 -6.9910749 0.0000000 16
Eagle SUPER AFR - EAS 0 -0.0027536 0.0001214 653.4378 -22.6835873 0.0000000 16
Eagle SUPER AFR - EUR 0 -0.0006338 0.0001058 653.4378 -5.9920944 0.0000000 16
Eagle SUPER AFR - SAS 0 -0.0017238 0.0001144 653.4378 -15.0738891 0.0000000 16
Eagle SUPER AMR - EAS 0 -0.0020691 0.0001287 653.4378 -16.0823202 0.0000000 16
Eagle SUPER AMR - EUR 0 0.0000508 0.0001140 653.4378 0.4454190 0.9918448 16
Eagle SUPER AMR - SAS 0 -0.0010392 0.0001220 653.4378 -8.5155143 0.0000000 16
Eagle SUPER EAS - EUR 0 0.0021198 0.0001347 653.4378 15.7347283 0.0000000 16
Eagle SUPER EAS - SAS 0 0.0010299 0.0001416 653.4378 7.2749511 0.0000000 16
Eagle SUPER EUR - SAS 0 -0.0010900 0.0001284 653.4378 -8.4877471 0.0000000 16
SHAPEIT SUPER AFR - AMR 0 -0.0007895 0.0000979 653.4378 -8.0622376 0.0000000 16
SHAPEIT SUPER AFR - EAS 0 -0.0025396 0.0001214 653.4378 -20.9205306 0.0000000 16
SHAPEIT SUPER AFR - EUR 0 -0.0006761 0.0001058 653.4378 -6.3923138 0.0000000 16
SHAPEIT SUPER AFR - SAS 0 -0.0017614 0.0001144 653.4378 -15.4030212 0.0000000 16
SHAPEIT SUPER AMR - EAS 0 -0.0017501 0.0001287 653.4378 -13.6034830 0.0000000 16
SHAPEIT SUPER AMR - EUR 0 0.0001133 0.0001140 653.4378 0.9940318 0.8580562 16
SHAPEIT SUPER AMR - SAS 0 -0.0009719 0.0001220 653.4378 -7.9644262 0.0000000 16
SHAPEIT SUPER EAS - EUR 0 0.0018635 0.0001347 653.4378 13.8319203 0.0000000 16
SHAPEIT SUPER EAS - SAS 0 0.0007782 0.0001416 653.4378 5.4972279 0.0000006 16
SHAPEIT SUPER EUR - SAS 0 -0.0010853 0.0001284 653.4378 -8.4511982 0.0000000 16
Beagle SUPER AFR - AMR 0 -0.0006515 0.0001001 650.1826 -6.5071736 0.0000000 17
Beagle SUPER AFR - EAS 0 -0.0026169 0.0001241 650.1826 -21.0828180 0.0000000 17
Beagle SUPER AFR - EUR 0 -0.0006443 0.0001081 650.1826 -5.9577574 0.0000000 17
Beagle SUPER AFR - SAS 0 -0.0018114 0.0001169 650.1826 -15.4919024 0.0000000 17
Beagle SUPER AMR - EAS 0 -0.0019654 0.0001315 650.1826 -14.9402023 0.0000000 17
Beagle SUPER AMR - EUR 0 0.0000072 0.0001166 650.1826 0.0617274 0.9999967 17
Beagle SUPER AMR - SAS 0 -0.0011599 0.0001248 650.1826 -9.2955037 0.0000000 17
Beagle SUPER EAS - EUR 0 0.0019726 0.0001378 650.1826 14.3193133 0.0000000 17
Beagle SUPER EAS - SAS 0 0.0008055 0.0001447 650.1826 5.5645944 0.0000004 17
Beagle SUPER EUR - SAS 0 -0.0011671 0.0001313 650.1826 -8.8882625 0.0000000 17
Eagle SUPER AFR - AMR 0 -0.0007019 0.0001001 650.1826 -7.0100132 0.0000000 17
Eagle SUPER AFR - EAS 0 -0.0029560 0.0001241 650.1826 -23.8146589 0.0000000 17
Eagle SUPER AFR - EUR 0 -0.0006728 0.0001081 650.1826 -6.2209768 0.0000000 17
Eagle SUPER AFR - SAS 0 -0.0020983 0.0001169 650.1826 -17.9452459 0.0000000 17
Eagle SUPER AMR - EAS 0 -0.0022541 0.0001315 650.1826 -17.1351420 0.0000000 17
Eagle SUPER AMR - EUR 0 0.0000291 0.0001166 650.1826 0.2493794 0.9991463 17
Eagle SUPER AMR - SAS 0 -0.0013964 0.0001248 650.1826 -11.1909603 0.0000000 17
Eagle SUPER EAS - EUR 0 0.0022832 0.0001378 650.1826 16.5741875 0.0000000 17
Eagle SUPER EAS - SAS 0 0.0008577 0.0001447 650.1826 5.9253957 0.0000000 17
Eagle SUPER EUR - SAS 0 -0.0014255 0.0001313 650.1826 -10.8561290 0.0000000 17
SHAPEIT SUPER AFR - AMR 0 -0.0006865 0.0001001 650.1826 -6.8567863 0.0000000 17
SHAPEIT SUPER AFR - EAS 0 -0.0027376 0.0001241 650.1826 -22.0556858 0.0000000 17
SHAPEIT SUPER AFR - EUR 0 -0.0006403 0.0001081 650.1826 -5.9202583 0.0000001 17
SHAPEIT SUPER AFR - SAS 0 -0.0017637 0.0001169 650.1826 -15.0835378 0.0000000 17
SHAPEIT SUPER AMR - EAS 0 -0.0020511 0.0001315 650.1826 -15.5920660 0.0000000 17
SHAPEIT SUPER AMR - EUR 0 0.0000463 0.0001166 650.1826 0.3967336 0.9947687 17
SHAPEIT SUPER AMR - SAS 0 -0.0010771 0.0001248 650.1826 -8.6323095 0.0000000 17
SHAPEIT SUPER EAS - EUR 0 0.0020974 0.0001378 650.1826 15.2253554 0.0000000 17
SHAPEIT SUPER EAS - SAS 0 0.0009740 0.0001447 650.1826 6.7287206 0.0000000 17
SHAPEIT SUPER EUR - SAS 0 -0.0011234 0.0001313 650.1826 -8.5555059 0.0000000 17
Beagle SUPER AFR - AMR 0 -0.0005757 0.0000783 663.0280 -7.3518272 0.0000000 18
Beagle SUPER AFR - EAS 0 -0.0021172 0.0000971 663.0280 -21.8100354 0.0000000 18
Beagle SUPER AFR - EUR 0 -0.0005734 0.0000846 663.0280 -6.7792484 0.0000000 18
Beagle SUPER AFR - SAS 0 -0.0014635 0.0000914 663.0280 -16.0042708 0.0000000 18
Beagle SUPER AMR - EAS 0 -0.0015415 0.0001029 663.0280 -14.9834938 0.0000000 18
Beagle SUPER AMR - EUR 0 0.0000023 0.0000912 663.0280 0.0250746 0.9999999 18
Beagle SUPER AMR - SAS 0 -0.0008878 0.0000976 663.0280 -9.0978713 0.0000000 18
Beagle SUPER EAS - EUR 0 0.0015438 0.0001077 663.0280 14.3296314 0.0000000 18
Beagle SUPER EAS - SAS 0 0.0006537 0.0001132 663.0280 5.7743071 0.0000001 18
Beagle SUPER EUR - SAS 0 -0.0008901 0.0001027 663.0280 -8.6679076 0.0000000 18
Eagle SUPER AFR - AMR 0 -0.0006346 0.0000783 663.0280 -8.1041081 0.0000000 18
Eagle SUPER AFR - EAS 0 -0.0025268 0.0000971 663.0280 -26.0298431 0.0000000 18
Eagle SUPER AFR - EUR 0 -0.0006685 0.0000846 663.0280 -7.9039036 0.0000000 18
Eagle SUPER AFR - SAS 0 -0.0016961 0.0000914 663.0280 -18.5480253 0.0000000 18
Eagle SUPER AMR - EAS 0 -0.0018922 0.0001029 663.0280 -18.3925675 0.0000000 18
Eagle SUPER AMR - EUR 0 -0.0000339 0.0000912 663.0280 -0.3721051 0.9959161 18
Eagle SUPER AMR - SAS 0 -0.0010615 0.0000976 663.0280 -10.8778961 0.0000000 18
Eagle SUPER EAS - EUR 0 0.0018583 0.0001077 663.0280 17.2489364 0.0000000 18
Eagle SUPER EAS - SAS 0 0.0008307 0.0001132 663.0280 7.3380322 0.0000000 18
Eagle SUPER EUR - SAS 0 -0.0010276 0.0001027 663.0280 -10.0067727 0.0000000 18
SHAPEIT SUPER AFR - AMR 0 -0.0006185 0.0000783 663.0280 -7.8983140 0.0000000 18
SHAPEIT SUPER AFR - EAS 0 -0.0022082 0.0000971 663.0280 -22.7481024 0.0000000 18
SHAPEIT SUPER AFR - EUR 0 -0.0006070 0.0000846 663.0280 -7.1761223 0.0000000 18
SHAPEIT SUPER AFR - SAS 0 -0.0014875 0.0000914 663.0280 -16.2661910 0.0000000 18
SHAPEIT SUPER AMR - EAS 0 -0.0015898 0.0001029 663.0280 -15.4526759 0.0000000 18
SHAPEIT SUPER AMR - EUR 0 0.0000115 0.0000912 663.0280 0.1262350 0.9999427 18
SHAPEIT SUPER AMR - SAS 0 -0.0008690 0.0000976 663.0280 -8.9048037 0.0000000 18
SHAPEIT SUPER EAS - EUR 0 0.0016013 0.0001077 663.0280 14.8632962 0.0000000 18
SHAPEIT SUPER EAS - SAS 0 0.0007208 0.0001132 663.0280 6.3671379 0.0000000 18
SHAPEIT SUPER EUR - SAS 0 -0.0008805 0.0001027 663.0280 -8.5742632 0.0000000 18
Beagle SUPER AFR - AMR 0 -0.0005653 0.0000918 666.2443 -6.1554178 0.0000000 19
Beagle SUPER AFR - EAS 0 -0.0024086 0.0001139 666.2443 -21.1560070 0.0000000 19
Beagle SUPER AFR - EUR 0 -0.0005226 0.0000992 666.2443 -5.2684408 0.0000018 19
Beagle SUPER AFR - SAS 0 -0.0015580 0.0001072 666.2443 -14.5267846 0.0000000 19
Beagle SUPER AMR - EAS 0 -0.0018433 0.0001207 666.2443 -15.2769893 0.0000000 19
Beagle SUPER AMR - EUR 0 0.0000427 0.0001069 666.2443 0.3990473 0.9946505 19
Beagle SUPER AMR - SAS 0 -0.0009927 0.0001145 666.2443 -8.6733780 0.0000000 19
Beagle SUPER EAS - EUR 0 0.0018860 0.0001264 666.2443 14.9264329 0.0000000 19
Beagle SUPER EAS - SAS 0 0.0008506 0.0001328 666.2443 6.4069730 0.0000000 19
Beagle SUPER EUR - SAS 0 -0.0010354 0.0001204 666.2443 -8.5965874 0.0000000 19
Eagle SUPER AFR - AMR 0 -0.0005826 0.0000918 666.2443 -6.3439089 0.0000000 19
Eagle SUPER AFR - EAS 0 -0.0027000 0.0001139 666.2443 -23.7153871 0.0000000 19
Eagle SUPER AFR - EUR 0 -0.0005104 0.0000992 666.2443 -5.1449956 0.0000035 19
Eagle SUPER AFR - SAS 0 -0.0016569 0.0001072 666.2443 -15.4490484 0.0000000 19
Eagle SUPER AMR - EAS 0 -0.0021174 0.0001207 666.2443 -17.5484586 0.0000000 19
Eagle SUPER AMR - EUR 0 0.0000722 0.0001069 666.2443 0.6754135 0.9616864 19
Eagle SUPER AMR - SAS 0 -0.0010743 0.0001145 666.2443 -9.3863511 0.0000000 19
Eagle SUPER EAS - EUR 0 0.0021896 0.0001264 666.2443 17.3294761 0.0000000 19
Eagle SUPER EAS - SAS 0 0.0010431 0.0001328 666.2443 7.8566854 0.0000000 19
Eagle SUPER EUR - SAS 0 -0.0011465 0.0001204 666.2443 -9.5195229 0.0000000 19
SHAPEIT SUPER AFR - AMR 0 -0.0006047 0.0000918 666.2443 -6.5850303 0.0000000 19
SHAPEIT SUPER AFR - EAS 0 -0.0025295 0.0001139 666.2443 -22.2178152 0.0000000 19
SHAPEIT SUPER AFR - EUR 0 -0.0005555 0.0000992 666.2443 -5.6002953 0.0000003 19
SHAPEIT SUPER AFR - SAS 0 -0.0016702 0.0001072 666.2443 -15.5734930 0.0000000 19
SHAPEIT SUPER AMR - EAS 0 -0.0019248 0.0001207 666.2443 -15.9518841 0.0000000 19
SHAPEIT SUPER AMR - EUR 0 0.0000492 0.0001069 666.2443 0.4601536 0.9907685 19
SHAPEIT SUPER AMR - SAS 0 -0.0010655 0.0001145 666.2443 -9.3094866 0.0000000 19
SHAPEIT SUPER EAS - EUR 0 0.0019740 0.0001264 666.2443 15.6226404 0.0000000 19
SHAPEIT SUPER EAS - SAS 0 0.0008593 0.0001328 666.2443 6.4719657 0.0000000 19
SHAPEIT SUPER EUR - SAS 0 -0.0011147 0.0001204 666.2443 -9.2553370 0.0000000 19
Beagle SUPER AFR - AMR 0 -0.0007722 0.0001025 652.0675 -7.5365726 0.0000000 20
Beagle SUPER AFR - EAS 0 -0.0027695 0.0001270 652.0675 -21.8029830 0.0000000 20
Beagle SUPER AFR - EUR 0 -0.0005905 0.0001107 652.0675 -5.3355198 0.0000013 20
Beagle SUPER AFR - SAS 0 -0.0017334 0.0001197 652.0675 -14.4864655 0.0000000 20
Beagle SUPER AMR - EAS 0 -0.0019973 0.0001346 652.0675 -14.8362259 0.0000000 20
Beagle SUPER AMR - EUR 0 0.0001817 0.0001193 652.0675 1.5228683 0.5479119 20
Beagle SUPER AMR - SAS 0 -0.0009612 0.0001277 652.0675 -7.5273517 0.0000000 20
Beagle SUPER EAS - EUR 0 0.0021790 0.0001410 652.0675 15.4567275 0.0000000 20
Beagle SUPER EAS - SAS 0 0.0010361 0.0001481 652.0675 6.9943358 0.0000000 20
Beagle SUPER EUR - SAS 0 -0.0011429 0.0001344 652.0675 -8.5054351 0.0000000 20
Eagle SUPER AFR - AMR 0 -0.0008697 0.0001025 652.0675 -8.4874557 0.0000000 20
Eagle SUPER AFR - EAS 0 -0.0030693 0.0001270 652.0675 -24.1633525 0.0000000 20
Eagle SUPER AFR - EUR 0 -0.0005752 0.0001107 652.0675 -5.1973791 0.0000027 20
Eagle SUPER AFR - SAS 0 -0.0019132 0.0001197 652.0675 -15.9888272 0.0000000 20
Eagle SUPER AMR - EAS 0 -0.0021997 0.0001346 652.0675 -16.3396442 0.0000000 20
Eagle SUPER AMR - EUR 0 0.0002944 0.0001193 652.0675 2.4675553 0.0993608 20
Eagle SUPER AMR - SAS 0 -0.0010435 0.0001277 652.0675 -8.1721665 0.0000000 20
Eagle SUPER EAS - EUR 0 0.0024941 0.0001410 652.0675 17.6919896 0.0000000 20
Eagle SUPER EAS - SAS 0 0.0011561 0.0001481 652.0675 7.8047927 0.0000000 20
Eagle SUPER EUR - SAS 0 -0.0013380 0.0001344 652.0675 -9.9570424 0.0000000 20
SHAPEIT SUPER AFR - AMR 0 -0.0008548 0.0001025 652.0675 -8.3429085 0.0000000 20
SHAPEIT SUPER AFR - EAS 0 -0.0028661 0.0001270 652.0675 -22.5636566 0.0000000 20
SHAPEIT SUPER AFR - EUR 0 -0.0006142 0.0001107 652.0675 -5.5490767 0.0000004 20
SHAPEIT SUPER AFR - SAS 0 -0.0017982 0.0001197 652.0675 -15.0279595 0.0000000 20
SHAPEIT SUPER AMR - EAS 0 -0.0020113 0.0001346 652.0675 -14.9402499 0.0000000 20
SHAPEIT SUPER AMR - EUR 0 0.0002407 0.0001193 652.0675 2.0172070 0.2588100 20
SHAPEIT SUPER AMR - SAS 0 -0.0009434 0.0001277 652.0675 -7.3877582 0.0000000 20
SHAPEIT SUPER EAS - EUR 0 0.0022520 0.0001410 652.0675 15.9744717 0.0000000 20
SHAPEIT SUPER EAS - SAS 0 0.0010679 0.0001481 652.0675 7.2092102 0.0000000 20
SHAPEIT SUPER EUR - SAS 0 -0.0011841 0.0001344 652.0675 -8.8117335 0.0000000 20
Beagle SUPER AFR - AMR 0 -0.0002164 0.0000976 696.3982 -2.2165641 0.1747130 21
Beagle SUPER AFR - EAS 0 -0.0016942 0.0001210 696.3982 -13.9967600 0.0000000 21
Beagle SUPER AFR - EUR 0 -0.0001822 0.0001055 696.3982 -1.7276072 0.4175899 21
Beagle SUPER AFR - SAS 0 -0.0011539 0.0001140 696.3982 -10.1199434 0.0000000 21
Beagle SUPER AMR - EAS 0 -0.0014778 0.0001283 696.3982 -11.5197383 0.0000000 21
Beagle SUPER AMR - EUR 0 0.0000342 0.0001137 696.3982 0.3009711 0.9982130 21
Beagle SUPER AMR - SAS 0 -0.0009375 0.0001217 696.3982 -7.7044437 0.0000000 21
Beagle SUPER EAS - EUR 0 0.0015120 0.0001343 696.3982 11.2554544 0.0000000 21
Beagle SUPER EAS - SAS 0 0.0005403 0.0001412 696.3982 3.8276206 0.0013258 21
Beagle SUPER EUR - SAS 0 -0.0009717 0.0001280 696.3982 -7.5887283 0.0000000 21
Eagle SUPER AFR - AMR 0 -0.0002526 0.0000976 696.3982 -2.5873233 0.0737863 21
Eagle SUPER AFR - EAS 0 -0.0020187 0.0001210 696.3982 -16.6779455 0.0000000 21
Eagle SUPER AFR - EUR 0 -0.0002613 0.0001055 696.3982 -2.4777356 0.0968707 21
Eagle SUPER AFR - SAS 0 -0.0013512 0.0001140 696.3982 -11.8505178 0.0000000 21
Eagle SUPER AMR - EAS 0 -0.0017661 0.0001283 696.3982 -13.7674105 0.0000000 21
Eagle SUPER AMR - EUR 0 -0.0000087 0.0001137 696.3982 -0.0764366 0.9999923 21
Eagle SUPER AMR - SAS 0 -0.0010986 0.0001217 696.3982 -9.0286020 0.0000000 21
Eagle SUPER EAS - EUR 0 0.0017574 0.0001343 696.3982 13.0824203 0.0000000 21
Eagle SUPER EAS - SAS 0 0.0006675 0.0001412 696.3982 4.7288336 0.0000269 21
Eagle SUPER EUR - SAS 0 -0.0010899 0.0001280 696.3982 -8.5119437 0.0000000 21
SHAPEIT SUPER AFR - AMR 0 -0.0003551 0.0000976 696.3982 -3.6365712 0.0027379 21
SHAPEIT SUPER AFR - EAS 0 -0.0017594 0.0001210 696.3982 -14.5360105 0.0000000 21
SHAPEIT SUPER AFR - EUR 0 -0.0002181 0.0001055 696.3982 -2.0678150 0.2353156 21
SHAPEIT SUPER AFR - SAS 0 -0.0012626 0.0001140 696.3982 -11.0732426 0.0000000 21
SHAPEIT SUPER AMR - EAS 0 -0.0014044 0.0001283 696.3982 -10.9477579 0.0000000 21
SHAPEIT SUPER AMR - EUR 0 0.0001370 0.0001137 696.3982 1.2048120 0.7486242 21
SHAPEIT SUPER AMR - SAS 0 -0.0009075 0.0001217 696.3982 -7.4583250 0.0000000 21
SHAPEIT SUPER EAS - EUR 0 0.0015414 0.0001343 696.3982 11.4742535 0.0000000 21
SHAPEIT SUPER EAS - SAS 0 0.0004969 0.0001412 696.3982 3.5199665 0.0041855 21
SHAPEIT SUPER EUR - SAS 0 -0.0010445 0.0001280 696.3982 -8.1574183 0.0000000 21
Beagle SUPER AFR - AMR 0 -0.0004068 0.0001265 677.1751 -3.2154756 0.0118738 22
Beagle SUPER AFR - EAS 0 -0.0025320 0.0001568 677.1751 -16.1443411 0.0000000 22
Beagle SUPER AFR - EUR 0 -0.0005019 0.0001366 677.1751 -3.6726859 0.0023985 22
Beagle SUPER AFR - SAS 0 -0.0016743 0.0001477 677.1751 -11.3328909 0.0000000 22
Beagle SUPER AMR - EAS 0 -0.0021252 0.0001662 677.1751 -12.7858221 0.0000000 22
Beagle SUPER AMR - EUR 0 -0.0000951 0.0001473 677.1751 -0.6454124 0.9674745 22
Beagle SUPER AMR - SAS 0 -0.0012675 0.0001577 677.1751 -8.0395209 0.0000000 22
Beagle SUPER EAS - EUR 0 0.0020301 0.0001741 677.1751 11.6634779 0.0000000 22
Beagle SUPER EAS - SAS 0 0.0008577 0.0001829 677.1751 4.6893952 0.0000326 22
Beagle SUPER EUR - SAS 0 -0.0011724 0.0001659 677.1751 -7.0667990 0.0000000 22
Eagle SUPER AFR - AMR 0 -0.0004200 0.0001265 677.1751 -3.3196563 0.0084076 22
Eagle SUPER AFR - EAS 0 -0.0028060 0.0001568 677.1751 -17.8915712 0.0000000 22
Eagle SUPER AFR - EUR 0 -0.0004205 0.0001366 677.1751 -3.0770329 0.0184482 22
Eagle SUPER AFR - SAS 0 -0.0017566 0.0001477 677.1751 -11.8900892 0.0000000 22
Eagle SUPER AMR - EAS 0 -0.0023860 0.0001662 677.1751 -14.3551479 0.0000000 22
Eagle SUPER AMR - EUR 0 -0.0000005 0.0001473 677.1751 -0.0034443 1.0000000 22
Eagle SUPER AMR - SAS 0 -0.0013367 0.0001577 677.1751 -8.4780557 0.0000000 22
Eagle SUPER EAS - EUR 0 0.0023855 0.0001741 677.1751 13.7054575 0.0000000 22
Eagle SUPER EAS - SAS 0 0.0010494 0.0001829 677.1751 5.7375731 0.0000001 22
Eagle SUPER EUR - SAS 0 -0.0013362 0.0001659 677.1751 -8.0535776 0.0000000 22
SHAPEIT SUPER AFR - AMR 0 -0.0005374 0.0001265 677.1751 -4.2480443 0.0002377 22
SHAPEIT SUPER AFR - EAS 0 -0.0025975 0.0001568 677.1751 -16.5620008 0.0000000 22
SHAPEIT SUPER AFR - EUR 0 -0.0006499 0.0001366 677.1751 -4.7556728 0.0000238 22
SHAPEIT SUPER AFR - SAS 0 -0.0017755 0.0001477 677.1751 -12.0175142 0.0000000 22
SHAPEIT SUPER AMR - EAS 0 -0.0020601 0.0001662 677.1751 -12.3940007 0.0000000 22
SHAPEIT SUPER AMR - EUR 0 -0.0001124 0.0001473 677.1751 -0.7632502 0.9409835 22
SHAPEIT SUPER AMR - SAS 0 -0.0012380 0.0001577 677.1751 -7.8525184 0.0000000 22
SHAPEIT SUPER EAS - EUR 0 0.0019476 0.0001741 677.1751 11.1895725 0.0000000 22
SHAPEIT SUPER EAS - SAS 0 0.0008220 0.0001829 677.1751 4.4945101 0.0000801 22
SHAPEIT SUPER EUR - SAS 0 -0.0011256 0.0001659 677.1751 -6.7844566 0.0000000 22
Beagle SUPER AFR - AMR 0 -0.0003326 0.0000593 1089.0700 -5.6083028 0.0000003 23
Beagle SUPER AFR - EAS 0 -0.0019472 0.0000593 1089.0700 -32.8312056 0.0000000 23
Beagle SUPER AFR - EUR 0 -0.0006228 0.0000593 1089.0700 -10.5014284 0.0000000 23
Beagle SUPER AFR - SAS 0 -0.0011571 0.0000593 1089.0700 -19.5101249 0.0000000 23
Beagle SUPER AMR - EAS 0 -0.0016146 0.0000593 1089.0700 -27.2229028 0.0000000 23
Beagle SUPER AMR - EUR 0 -0.0002902 0.0000593 1089.0700 -4.8931256 0.0000113 23
Beagle SUPER AMR - SAS 0 -0.0008245 0.0000593 1089.0700 -13.9018222 0.0000000 23
Beagle SUPER EAS - EUR 0 0.0013244 0.0000593 1089.0700 22.3297772 0.0000000 23
Beagle SUPER EAS - SAS 0 0.0007901 0.0000593 1089.0700 13.3210806 0.0000000 23
Beagle SUPER EUR - SAS 0 -0.0005343 0.0000593 1089.0700 -9.0086966 0.0000000 23
Eagle SUPER AFR - AMR 0 -0.0003202 0.0000593 1089.0700 -5.3985365 0.0000008 23
Eagle SUPER AFR - EAS 0 -0.0023056 0.0000593 1089.0700 -38.8734268 0.0000000 23
Eagle SUPER AFR - EUR 0 -0.0007077 0.0000593 1089.0700 -11.9330217 0.0000000 23
Eagle SUPER AFR - SAS 0 -0.0013356 0.0000593 1089.0700 -22.5189925 0.0000000 23
Eagle SUPER AMR - EAS 0 -0.0019854 0.0000593 1089.0700 -33.4748903 0.0000000 23
Eagle SUPER AMR - EUR 0 -0.0003876 0.0000593 1089.0700 -6.5344852 0.0000000 23
Eagle SUPER AMR - SAS 0 -0.0010154 0.0000593 1089.0700 -17.1204559 0.0000000 23
Eagle SUPER EAS - EUR 0 0.0015978 0.0000593 1089.0700 26.9404051 0.0000000 23
Eagle SUPER EAS - SAS 0 0.0009700 0.0000593 1089.0700 16.3544343 0.0000000 23
Eagle SUPER EUR - SAS 0 -0.0006278 0.0000593 1089.0700 -10.5859707 0.0000000 23
SHAPEIT SUPER AFR - AMR 0 -0.0003732 0.0000593 1089.0700 -6.2929479 0.0000000 23
SHAPEIT SUPER AFR - EAS 0 -0.0018829 0.0000593 1089.0700 -31.7473628 0.0000000 23
SHAPEIT SUPER AFR - EUR 0 -0.0006244 0.0000593 1089.0700 -10.5276276 0.0000000 23
SHAPEIT SUPER AFR - SAS 0 -0.0010932 0.0000593 1089.0700 -18.4315950 0.0000000 23
SHAPEIT SUPER AMR - EAS 0 -0.0015097 0.0000593 1089.0700 -25.4544149 0.0000000 23
SHAPEIT SUPER AMR - EUR 0 -0.0002512 0.0000593 1089.0700 -4.2346797 0.0002401 23
SHAPEIT SUPER AMR - SAS 0 -0.0007199 0.0000593 1089.0700 -12.1386471 0.0000000 23
SHAPEIT SUPER EAS - EUR 0 0.0012585 0.0000593 1089.0700 21.2197352 0.0000000 23
SHAPEIT SUPER EAS - SAS 0 0.0007898 0.0000593 1089.0700 13.3157679 0.0000000 23
SHAPEIT SUPER EUR - SAS 0 -0.0004688 0.0000593 1089.0700 -7.9039673 0.0000000 23

Flip Errors

# df_flips <- df_switch_trio[[1]] %>%
#   mutate(Eagle = (n_flip_eagle) / n_hets,
#          Beagle = (n_flip_beagle) / n_hets,
#          SHAPEIT = (n_flip_shapeit) / n_hets) %>%
#   select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#   mutate(chrom = 1)
# 
# for(i in 2:22){
#   df_flips <- bind_rows(df_flips, 
#                         {
#                           df_switch_trio[[i]] %>%
#                             mutate(Eagle = (n_flip_eagle) / n_hets,
#                                    Beagle = (n_flip_beagle) / n_hets,
#                                    SHAPEIT = (n_flip_shapeit) / n_hets) %>%
#                             select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#                             mutate(chrom = i)
#                         })
# }

df_flips <- df_switch_trio_noth %>%
  mutate(Eagle = (n_flip_e) / n_het,
         Beagle = (n_flip_b) / n_het,
         SHAPEIT = (n_flip_s) / n_het) %>%
  select(Eagle, Beagle, SHAPEIT, sample, chrom)

df_flips <- df_flips %>%
  left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
  rename(pair_id = sample) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)

df_flips <- df_flips %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_flip_eagle) / n_hets,
             Beagle = (n_flip_beagle) / n_hets,
             SHAPEIT = (n_flip_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

df_flips %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable()
chrom Beagle Eagle SHAPEIT
1 0.0057436 0.0049992 0.0062407
2 0.0058785 0.0050772 0.0064003
3 0.0055282 0.0047878 0.0060123
4 0.0052003 0.0045228 0.0056534
5 0.0055357 0.0048034 0.0060346
6 0.0050140 0.0043553 0.0054361
7 0.0055456 0.0048417 0.0060457
8 0.0055975 0.0048655 0.0061065
9 0.0061151 0.0053432 0.0066371
10 0.0054473 0.0047538 0.0059287
11 0.0055329 0.0048044 0.0060011
12 0.0055251 0.0047841 0.0060263
13 0.0052888 0.0045885 0.0057716
14 0.0057178 0.0050183 0.0062432
15 0.0061150 0.0053937 0.0066694
16 0.0064066 0.0055367 0.0069591
17 0.0063643 0.0056145 0.0069171
18 0.0055085 0.0047830 0.0060110
19 0.0059452 0.0051986 0.0064004
20 0.0060847 0.0053683 0.0065812
21 0.0060175 0.0054222 0.0065460
22 0.0066474 0.0060262 0.0071902
23 0.0013794 0.0013749 0.0015596
df_flips %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable() 
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
chrom SUPER Beagle Eagle SHAPEIT
1 AFR 0.0048509 0.0038606 0.0052944
1 AMR 0.0055828 0.0049953 0.0061469
1 EAS 0.0074943 0.0068074 0.0080115
1 EUR 0.0054117 0.0049288 0.0057730
1 SAS 0.0070490 0.0062545 0.0077186
2 AFR 0.0049356 0.0039058 0.0054038
2 AMR 0.0058569 0.0051911 0.0063823
2 EAS 0.0076922 0.0070001 0.0083523
2 EUR 0.0053915 0.0048466 0.0058080
2 SAS 0.0072199 0.0063251 0.0078776
3 AFR 0.0046336 0.0036385 0.0050852
3 AMR 0.0054302 0.0048384 0.0059500
3 EAS 0.0072600 0.0065980 0.0077701
3 EUR 0.0052122 0.0047396 0.0055768
3 SAS 0.0067326 0.0059511 0.0073641
4 AFR 0.0043179 0.0034037 0.0047116
4 AMR 0.0052432 0.0047134 0.0057537
4 EAS 0.0066767 0.0061394 0.0072441
4 EUR 0.0048553 0.0043933 0.0052107
4 SAS 0.0064016 0.0056557 0.0069288
5 AFR 0.0046907 0.0036968 0.0051276
5 AMR 0.0053647 0.0048383 0.0059255
5 EAS 0.0071985 0.0065383 0.0078239
5 EUR 0.0051649 0.0046727 0.0055210
5 SAS 0.0068679 0.0060593 0.0074859
6 AFR 0.0042879 0.0034016 0.0046848
6 AMR 0.0049184 0.0044419 0.0053747
6 EAS 0.0065134 0.0059035 0.0069773
6 EUR 0.0045903 0.0041417 0.0048986
6 SAS 0.0061483 0.0054287 0.0066827
7 AFR 0.0047125 0.0038187 0.0052157
7 AMR 0.0054486 0.0048671 0.0059390
7 EAS 0.0072970 0.0066100 0.0078103
7 EUR 0.0050546 0.0046022 0.0054386
7 SAS 0.0068066 0.0060233 0.0074503
8 AFR 0.0046627 0.0036525 0.0051578
8 AMR 0.0055686 0.0050487 0.0061625
8 EAS 0.0074901 0.0067916 0.0079265
8 EUR 0.0051737 0.0046984 0.0055363
8 SAS 0.0067852 0.0060173 0.0074357
9 AFR 0.0053080 0.0042986 0.0058223
9 AMR 0.0058838 0.0052889 0.0064634
9 EAS 0.0079478 0.0072104 0.0084824
9 EUR 0.0057032 0.0051775 0.0060412
9 SAS 0.0073625 0.0065280 0.0080306
10 AFR 0.0047047 0.0037686 0.0051588
10 AMR 0.0053361 0.0047940 0.0058426
10 EAS 0.0069913 0.0063791 0.0075465
10 EUR 0.0050001 0.0045181 0.0053389
10 SAS 0.0066376 0.0059388 0.0072602
11 AFR 0.0046181 0.0036593 0.0050623
11 AMR 0.0055062 0.0049217 0.0059881
11 EAS 0.0071875 0.0065083 0.0077529
11 EUR 0.0050552 0.0045970 0.0054001
11 SAS 0.0069390 0.0061409 0.0075149
12 AFR 0.0046534 0.0036729 0.0051003
12 AMR 0.0054161 0.0048634 0.0059321
12 EAS 0.0071733 0.0065287 0.0077276
12 EUR 0.0050806 0.0045860 0.0054733
12 SAS 0.0069257 0.0060555 0.0076233
13 AFR 0.0045223 0.0035729 0.0049646
13 AMR 0.0051376 0.0045220 0.0056553
13 EAS 0.0068749 0.0062732 0.0073886
13 EUR 0.0049592 0.0044487 0.0052886
13 SAS 0.0064168 0.0058462 0.0071055
14 AFR 0.0048613 0.0039247 0.0053367
14 AMR 0.0058033 0.0051849 0.0063353
14 EAS 0.0072085 0.0066774 0.0078172
14 EUR 0.0052080 0.0047903 0.0056560
14 SAS 0.0069843 0.0062172 0.0076441
15 AFR 0.0052719 0.0043389 0.0057695
15 AMR 0.0058980 0.0052902 0.0064864
15 EAS 0.0078680 0.0071805 0.0084877
15 EUR 0.0057784 0.0052837 0.0061797
15 SAS 0.0073972 0.0066798 0.0081686
16 AFR 0.0054590 0.0044255 0.0059674
16 AMR 0.0062847 0.0055285 0.0068819
16 EAS 0.0083862 0.0075083 0.0089120
16 EUR 0.0058224 0.0053356 0.0063845
16 SAS 0.0079026 0.0067608 0.0084978
17 AFR 0.0053959 0.0044922 0.0059663
17 AMR 0.0061923 0.0055368 0.0067498
17 EAS 0.0084273 0.0076490 0.0089135
17 EUR 0.0058933 0.0053589 0.0063126
17 SAS 0.0077768 0.0069920 0.0085050
18 AFR 0.0045757 0.0036446 0.0050768
18 AMR 0.0055084 0.0048932 0.0060666
18 EAS 0.0072546 0.0065974 0.0077358
18 EUR 0.0051053 0.0046441 0.0054570
18 SAS 0.0067430 0.0059354 0.0073668
19 AFR 0.0050913 0.0041413 0.0055110
19 AMR 0.0058473 0.0052828 0.0063396
19 EAS 0.0077344 0.0069670 0.0082385
19 EUR 0.0055367 0.0050112 0.0058588
19 SAS 0.0071206 0.0063006 0.0077262
20 AFR 0.0050893 0.0041390 0.0055168
20 AMR 0.0060918 0.0054615 0.0066459
20 EAS 0.0080383 0.0074367 0.0086405
20 EUR 0.0055472 0.0051462 0.0059501
20 SAS 0.0074489 0.0066526 0.0080439
21 AFR 0.0053831 0.0045895 0.0059090
21 AMR 0.0059039 0.0054901 0.0064466
21 EAS 0.0073858 0.0067774 0.0078760
21 EUR 0.0055923 0.0051591 0.0060380
21 SAS 0.0070768 0.0064655 0.0077258
22 AFR 0.0059118 0.0050632 0.0064401
22 AMR 0.0065342 0.0060244 0.0070762
22 EAS 0.0082989 0.0077582 0.0088412
22 EUR 0.0060571 0.0056668 0.0064708
22 SAS 0.0079135 0.0072917 0.0086547
23 AFR 0.0010081 0.0009991 0.0011945
23 AMR 0.0011009 0.0010802 0.0012704
23 EAS 0.0019555 0.0019427 0.0021114
23 EUR 0.0012423 0.0012304 0.0014230
23 SAS 0.0015903 0.0016220 0.0017988
df_flips %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Flip Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_flips$chrom)), breaks = unique(df_flips$chrom))

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
df_flips %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Flip Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_flips$chrom)), breaks = unique(df_flips$chrom))
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
d7d8f5a Andy Beck 2024-05-22
da672c2 Andy Beck 2024-05-22
# Beagle
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(Beagle)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00438   0.00576   0.00138      207.       0     2957.  0.00434   0.00442
# ℹ 2 more variables: method <chr>, alternative <chr>
# Eagle
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00367   0.00504   0.00137      176.       0     3336.  0.00362   0.00371
# ℹ 2 more variables: method <chr>, alternative <chr>
# SHAPEIT
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00470   0.00626   0.00156      217.       0     2802.  0.00466   0.00475
# ℹ 2 more variables: method <chr>, alternative <chr>
mod_fit <- df_flips %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)

for(i in 2:23){
  mod_fit <- df_flips %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
  
  df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pairwise <- df_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}

df_anova %>%
  knitr::kable()
term sumsq meansq NumDF DenDF statistic p.value chrom
method 0.0004701 0.0002351 2 1202 3013.4749 0 1
method 0.0005348 0.0002674 2 1202 3318.1790 0 2
method 0.0004579 0.0002290 2 1202 3011.9306 0 3
method 0.0003898 0.0001949 2 1202 2569.4671 0 4
method 0.0004617 0.0002308 2 1202 2718.1027 0 5
method 0.0003572 0.0001786 2 1202 2679.0043 0 6
method 0.0004406 0.0002203 2 1202 2572.5825 0 7
method 0.0004686 0.0002343 2 1202 2046.3998 0 8
method 0.0005101 0.0002551 2 1202 2506.4370 0 9
method 0.0004200 0.0002100 2 1202 2375.3062 0 10
method 0.0004379 0.0002189 2 1202 2188.9479 0 11
method 0.0004703 0.0002351 2 1202 2259.7295 0 12
method 0.0004261 0.0002130 2 1202 1679.8712 0 13
method 0.0004547 0.0002273 2 1202 1921.3314 0 14
method 0.0004926 0.0002463 2 1202 1943.4193 0 15
method 0.0006191 0.0003095 2 1202 1781.7578 0 16
method 0.0005146 0.0002573 2 1202 1661.9270 0 17
method 0.0004589 0.0002294 2 1202 1880.3071 0 18
method 0.0004433 0.0002216 2 1202 1421.4820 0 19
method 0.0004476 0.0002238 2 1202 1429.7051 0 20
method 0.0003806 0.0001903 2 1202 991.8020 0 21
method 0.0004084 0.0002042 2 1202 887.5711 0 22
method 0.0000222 0.0000111 2 1998 638.9949 0 23
df_pairwise %>%
  knitr::kable()
term contrast null.value estimate std.error df statistic adj.p.value chrom
method Beagle - Eagle 0 0.0007445 1.61e-05 1202 46.2469554 0.0000000 1
method Beagle - SHAPEIT 0 -0.0004971 1.61e-05 1202 -30.8776948 0.0000000 1
method Eagle - SHAPEIT 0 -0.0012416 1.61e-05 1202 -77.1246502 0.0000000 1
method Beagle - Eagle 0 0.0008013 1.64e-05 1202 48.9749823 0.0000000 2
method Beagle - SHAPEIT 0 -0.0005218 1.64e-05 1202 -31.8894262 0.0000000 2
method Eagle - SHAPEIT 0 -0.0013231 1.64e-05 1202 -80.8644085 0.0000000 2
method Beagle - Eagle 0 0.0007405 1.59e-05 1202 46.5936902 0.0000000 3
method Beagle - SHAPEIT 0 -0.0004840 1.59e-05 1202 -30.4587775 0.0000000 3
method Eagle - SHAPEIT 0 -0.0012245 1.59e-05 1202 -77.0524677 0.0000000 3
method Beagle - Eagle 0 0.0006775 1.59e-05 1202 42.6785421 0.0000000 4
method Beagle - SHAPEIT 0 -0.0004531 1.59e-05 1202 -28.5416595 0.0000000 4
method Eagle - SHAPEIT 0 -0.0011306 1.59e-05 1202 -71.2202016 0.0000000 4
method Beagle - Eagle 0 0.0007323 1.68e-05 1202 43.5946151 0.0000000 5
method Beagle - SHAPEIT 0 -0.0004988 1.68e-05 1202 -29.6981900 0.0000000 5
method Eagle - SHAPEIT 0 -0.0012311 1.68e-05 1202 -73.2928051 0.0000000 5
method Beagle - Eagle 0 0.0006586 1.49e-05 1202 44.2577383 0.0000000 6
method Beagle - SHAPEIT 0 -0.0004221 1.49e-05 1202 -28.3631688 0.0000000 6
method Eagle - SHAPEIT 0 -0.0010807 1.49e-05 1202 -72.6209071 0.0000000 6
method Beagle - Eagle 0 0.0007039 1.69e-05 1202 41.7366488 0.0000000 7
method Beagle - SHAPEIT 0 -0.0005001 1.69e-05 1202 -29.6530856 0.0000000 7
method Eagle - SHAPEIT 0 -0.0012041 1.69e-05 1202 -71.3897344 0.0000000 7
method Beagle - Eagle 0 0.0007321 1.95e-05 1202 37.5369195 0.0000000 8
method Beagle - SHAPEIT 0 -0.0005089 1.95e-05 1202 -26.0961643 0.0000000 8
method Eagle - SHAPEIT 0 -0.0012410 1.95e-05 1202 -63.6330838 0.0000000 8
method Beagle - Eagle 0 0.0007718 1.84e-05 1202 41.9768441 0.0000000 9
method Beagle - SHAPEIT 0 -0.0005220 1.84e-05 1202 -28.3888396 0.0000000 9
method Eagle - SHAPEIT 0 -0.0012938 1.84e-05 1202 -70.3656836 0.0000000 9
method Beagle - Eagle 0 0.0006935 1.71e-05 1202 40.4636630 0.0000000 10
method Beagle - SHAPEIT 0 -0.0004814 1.71e-05 1202 -28.0897810 0.0000000 10
method Eagle - SHAPEIT 0 -0.0011749 1.71e-05 1202 -68.5534440 0.0000000 10
method Beagle - Eagle 0 0.0007285 1.82e-05 1202 39.9658214 0.0000000 11
method Beagle - SHAPEIT 0 -0.0004682 1.82e-05 1202 -25.6840547 0.0000000 11
method Eagle - SHAPEIT 0 -0.0011967 1.82e-05 1202 -65.6498761 0.0000000 11
method Beagle - Eagle 0 0.0007410 1.86e-05 1202 39.8553280 0.0000000 12
method Beagle - SHAPEIT 0 -0.0005012 1.86e-05 1202 -26.9579298 0.0000000 12
method Eagle - SHAPEIT 0 -0.0012422 1.86e-05 1202 -66.8132578 0.0000000 12
method Beagle - Eagle 0 0.0007003 2.05e-05 1202 34.1204928 0.0000000 13
method Beagle - SHAPEIT 0 -0.0004827 2.05e-05 1202 -23.5186982 0.0000000 13
method Eagle - SHAPEIT 0 -0.0011831 2.05e-05 1202 -57.6391910 0.0000000 13
method Beagle - Eagle 0 0.0006995 1.98e-05 1202 35.2821507 0.0000000 14
method Beagle - SHAPEIT 0 -0.0005254 1.98e-05 1202 -26.4993205 0.0000000 14
method Eagle - SHAPEIT 0 -0.0012249 1.98e-05 1202 -61.7814712 0.0000000 14
method Beagle - Eagle 0 0.0007213 2.05e-05 1202 35.1503531 0.0000000 15
method Beagle - SHAPEIT 0 -0.0005544 2.05e-05 1202 -27.0170709 0.0000000 15
method Eagle - SHAPEIT 0 -0.0012757 2.05e-05 1202 -62.1674240 0.0000000 15
method Beagle - Eagle 0 0.0008699 2.40e-05 1202 36.2100322 0.0000000 16
method Beagle - SHAPEIT 0 -0.0005525 2.40e-05 1202 -22.9956142 0.0000000 16
method Eagle - SHAPEIT 0 -0.0014224 2.40e-05 1202 -59.2056464 0.0000000 16
method Beagle - Eagle 0 0.0007498 2.27e-05 1202 33.0596397 0.0000000 17
method Beagle - SHAPEIT 0 -0.0005528 2.27e-05 1202 -24.3747719 0.0000000 17
method Eagle - SHAPEIT 0 -0.0013026 2.27e-05 1202 -57.4344116 0.0000000 17
method Beagle - Eagle 0 0.0007255 2.01e-05 1202 36.0323784 0.0000000 18
method Beagle - SHAPEIT 0 -0.0005025 2.01e-05 1202 -24.9571910 0.0000000 18
method Eagle - SHAPEIT 0 -0.0012280 2.01e-05 1202 -60.9895694 0.0000000 18
method Beagle - Eagle 0 0.0007466 2.28e-05 1202 32.8036707 0.0000000 19
method Beagle - SHAPEIT 0 -0.0004552 2.28e-05 1202 -20.0009441 0.0000000 19
method Eagle - SHAPEIT 0 -0.0012018 2.28e-05 1202 -52.8046148 0.0000000 19
method Beagle - Eagle 0 0.0007164 2.28e-05 1202 31.4130234 0.0000000 20
method Beagle - SHAPEIT 0 -0.0004965 2.28e-05 1202 -21.7698034 0.0000000 20
method Eagle - SHAPEIT 0 -0.0012129 2.28e-05 1202 -53.1828268 0.0000000 20
method Beagle - Eagle 0 0.0005952 2.52e-05 1202 23.5757485 0.0000000 21
method Beagle - SHAPEIT 0 -0.0005286 2.52e-05 1202 -20.9358326 0.0000000 21
method Eagle - SHAPEIT 0 -0.0011238 2.52e-05 1202 -44.5115811 0.0000000 21
method Beagle - Eagle 0 0.0006212 2.76e-05 1202 22.4682068 0.0000000 22
method Beagle - SHAPEIT 0 -0.0005428 2.76e-05 1202 -19.6324060 0.0000000 22
method Eagle - SHAPEIT 0 -0.0011640 2.76e-05 1202 -42.1006129 0.0000000 22
method Beagle - Eagle 0 0.0000045 5.90e-06 1998 0.7705121 0.7211872 23
method Beagle - SHAPEIT 0 -0.0001802 5.90e-06 1998 -30.5670808 0.0000000 23
method Eagle - SHAPEIT 0 -0.0001848 5.90e-06 1998 -31.3375929 0.0000000 23
mod_fit <- df_flips %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}

df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)

for(i in 2:23){
  mod_fit <- df_flips %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
  
  df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
  df_pop_pop <- df_pop_pop %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}

df_pop_anova %>%
  knitr::kable()
term sumsq meansq NumDF DenDF statistic p.value chrom
method 0.0003967 0.0001983 2 1194.0000 3192.826276 0.0000000 1
SUPER 0.0000276 0.0000069 4 597.0000 111.269503 0.0000000 1
method:SUPER 0.0000196 0.0000024 8 1194.0000 39.413286 0.0000000 1
method 0.0004588 0.0002294 2 1194.0000 3464.684510 0.0000000 2
SUPER 0.0000327 0.0000082 4 597.0000 123.522649 0.0000000 2
method:SUPER 0.0000178 0.0000022 8 1194.0000 33.617845 0.0000000 2
method 0.0003820 0.0001910 2 1194.0000 3181.378464 0.0000000 3
SUPER 0.0000271 0.0000068 4 597.0000 112.819852 0.0000000 3
method:SUPER 0.0000197 0.0000025 8 1194.0000 40.986641 0.0000000 3
method 0.0003275 0.0001637 2 1194.0000 2558.720305 0.0000000 4
SUPER 0.0000312 0.0000078 4 597.0000 121.768081 0.0000000 4
method:SUPER 0.0000148 0.0000018 8 1194.0000 28.856281 0.0000000 4
method 0.0003935 0.0001968 2 1194.0000 2891.005556 0.0000000 5
SUPER 0.0000287 0.0000072 4 597.0000 105.490039 0.0000000 5
method:SUPER 0.0000208 0.0000026 8 1194.0000 38.224530 0.0000000 5
method 0.0003006 0.0001503 2 1194.0000 2799.000055 0.0000000 6
SUPER 0.0000219 0.0000055 4 597.0000 101.834616 0.0000000 6
method:SUPER 0.0000160 0.0000020 8 1194.0000 37.296767 0.0000000 6
method 0.0003749 0.0001874 2 1194.0000 2578.764416 0.0000000 7
SUPER 0.0000327 0.0000082 4 597.0000 112.299606 0.0000000 7
method:SUPER 0.0000161 0.0000020 8 1194.0000 27.745892 0.0000000 7
method 0.0003851 0.0001926 2 1194.0000 2020.831393 0.0000000 8
SUPER 0.0000425 0.0000106 4 597.0000 111.515524 0.0000000 8
method:SUPER 0.0000238 0.0000030 8 1194.0000 31.262187 0.0000000 8
method 0.0004287 0.0002143 2 1194.0000 2538.806313 0.0000000 9
SUPER 0.0000345 0.0000086 4 597.0000 102.026700 0.0000000 9
method:SUPER 0.0000215 0.0000027 8 1194.0000 31.857680 0.0000000 9
method 0.0003517 0.0001759 2 1194.0000 2356.376792 0.0000000 10
SUPER 0.0000328 0.0000082 4 596.9999 109.877832 0.0000000 10
method:SUPER 0.0000172 0.0000021 8 1194.0000 28.739506 0.0000000 10
method 0.0003711 0.0001855 2 1194.0000 2178.697681 0.0000000 11
SUPER 0.0000366 0.0000091 4 597.0000 107.358104 0.0000000 11
method:SUPER 0.0000185 0.0000023 8 1194.0000 27.220855 0.0000000 11
method 0.0004031 0.0002016 2 1194.0000 2319.701014 0.0000000 12
SUPER 0.0000358 0.0000090 4 596.9999 103.017010 0.0000000 12
method:SUPER 0.0000213 0.0000027 8 1194.0000 30.677480 0.0000000 12
method 0.0003504 0.0001752 2 1194.0000 1535.886331 0.0000000 13
SUPER 0.0000432 0.0000108 4 597.0000 94.754693 0.0000000 13
method:SUPER 0.0000162 0.0000020 8 1194.0000 17.764775 0.0000000 13
method 0.0003811 0.0001906 2 1194.0000 1821.579291 0.0000000 14
SUPER 0.0000400 0.0000100 4 597.0000 95.492420 0.0000000 14
method:SUPER 0.0000173 0.0000022 8 1194.0000 20.672648 0.0000000 14
method 0.0004234 0.0002117 2 1194.0000 1858.557476 0.0000000 15
SUPER 0.0000414 0.0000104 4 597.0000 90.917098 0.0000000 15
method:SUPER 0.0000163 0.0000020 8 1194.0000 17.932999 0.0000000 15
method 0.0005389 0.0002695 2 1194.0000 1694.618761 0.0000000 16
SUPER 0.0000573 0.0000143 4 597.0000 90.099898 0.0000000 16
method:SUPER 0.0000190 0.0000024 8 1194.0000 14.913350 0.0000000 16
method 0.0004385 0.0002193 2 1194.0000 1515.063291 0.0000000 17
SUPER 0.0000544 0.0000136 4 597.0000 93.955710 0.0000000 17
method:SUPER 0.0000133 0.0000017 8 1194.0000 11.491384 0.0000000 17
method 0.0003825 0.0001913 2 1194.0000 1774.755328 0.0000000 18
SUPER 0.0000479 0.0000120 4 597.0000 111.168244 0.0000000 18
method:SUPER 0.0000180 0.0000023 8 1194.0000 20.880766 0.0000000 18
method 0.0003829 0.0001915 2 1194.0000 1337.730530 0.0000000 19
SUPER 0.0000500 0.0000125 4 597.0000 87.270523 0.0000000 19
method:SUPER 0.0000165 0.0000021 8 1194.0000 14.436580 0.0000000 19
method 0.0003781 0.0001890 2 1194.0000 1327.232824 0.0000000 20
SUPER 0.0000550 0.0000137 4 597.0000 96.500071 0.0000000 20
method:SUPER 0.0000181 0.0000023 8 1194.0000 15.887647 0.0000000 20
method 0.0003217 0.0001609 2 1194.0000 879.761890 0.0000000 21
SUPER 0.0000411 0.0000103 4 597.0000 56.153871 0.0000000 21
method:SUPER 0.0000123 0.0000015 8 1194.0000 8.418774 0.0000000 21
method 0.0003411 0.0001706 2 1194.0000 785.671346 0.0000000 22
SUPER 0.0000543 0.0000136 4 597.0000 62.530883 0.0000000 22
method:SUPER 0.0000173 0.0000022 8 1194.0000 9.977930 0.0000000 22
method 0.0000222 0.0000111 2 1990.0000 641.105027 0.0000000 23
SUPER 0.0000178 0.0000044 4 995.0000 256.572985 0.0000000 23
method:SUPER 0.0000003 0.0000000 8 1990.0000 1.824723 0.0681454 23
df_pop_pairwise %>% knitr::kable()
SUPER term contrast null.value estimate std.error df statistic adj.p.value chrom
AFR method Beagle - Eagle 0 0.0009903 2.49e-05 1194 39.8313731 0.0000000 1
AFR method Beagle - SHAPEIT 0 -0.0004435 2.49e-05 1194 -17.8370961 0.0000000 1
AFR method Eagle - SHAPEIT 0 -0.0014338 2.49e-05 1194 -57.6684692 0.0000000 1
AMR method Beagle - Eagle 0 0.0005874 3.01e-05 1194 19.5069897 0.0000000 1
AMR method Beagle - SHAPEIT 0 -0.0005642 3.01e-05 1194 -18.7336247 0.0000000 1
AMR method Eagle - SHAPEIT 0 -0.0011516 3.01e-05 1194 -38.2406145 0.0000000 1
EAS method Beagle - Eagle 0 0.0006869 4.15e-05 1194 16.5360004 0.0000000 1
EAS method Beagle - SHAPEIT 0 -0.0005172 4.15e-05 1194 -12.4506624 0.0000000 1
EAS method Eagle - SHAPEIT 0 -0.0012041 4.15e-05 1194 -28.9866628 0.0000000 1
EUR method Beagle - Eagle 0 0.0004829 3.41e-05 1194 14.1700951 0.0000000 1
EUR method Beagle - SHAPEIT 0 -0.0003613 3.41e-05 1194 -10.6031851 0.0000000 1
EUR method Eagle - SHAPEIT 0 -0.0008442 3.41e-05 1194 -24.7732801 0.0000000 1
SAS method Beagle - Eagle 0 0.0007945 3.82e-05 1194 20.7802550 0.0000000 1
SAS method Beagle - SHAPEIT 0 -0.0006696 3.82e-05 1194 -17.5129608 0.0000000 1
SAS method Eagle - SHAPEIT 0 -0.0014640 3.82e-05 1194 -38.2932157 0.0000000 1
AFR method Beagle - Eagle 0 0.0010298 2.57e-05 1194 40.1220106 0.0000000 2
AFR method Beagle - SHAPEIT 0 -0.0004682 2.57e-05 1194 -18.2433930 0.0000000 2
AFR method Eagle - SHAPEIT 0 -0.0014980 2.57e-05 1194 -58.3654037 0.0000000 2
AMR method Beagle - Eagle 0 0.0006658 3.11e-05 1194 21.4151192 0.0000000 2
AMR method Beagle - SHAPEIT 0 -0.0005254 3.11e-05 1194 -16.9002652 0.0000000 2
AMR method Eagle - SHAPEIT 0 -0.0011912 3.11e-05 1194 -38.3153843 0.0000000 2
EAS method Beagle - Eagle 0 0.0006921 4.29e-05 1194 16.1382729 0.0000000 2
EAS method Beagle - SHAPEIT 0 -0.0006601 4.29e-05 1194 -15.3916948 0.0000000 2
EAS method Eagle - SHAPEIT 0 -0.0013521 4.29e-05 1194 -31.5299677 0.0000000 2
EUR method Beagle - Eagle 0 0.0005449 3.52e-05 1194 15.4903048 0.0000000 2
EUR method Beagle - SHAPEIT 0 -0.0004166 3.52e-05 1194 -11.8414627 0.0000000 2
EUR method Eagle - SHAPEIT 0 -0.0009615 3.52e-05 1194 -27.3317674 0.0000000 2
SAS method Beagle - Eagle 0 0.0008948 3.95e-05 1194 22.6702712 0.0000000 2
SAS method Beagle - SHAPEIT 0 -0.0006577 3.95e-05 1194 -16.6646840 0.0000000 2
SAS method Eagle - SHAPEIT 0 -0.0015525 3.95e-05 1194 -39.3349552 0.0000000 2
AFR method Beagle - Eagle 0 0.0009951 2.44e-05 1194 40.7119464 0.0000000 3
AFR method Beagle - SHAPEIT 0 -0.0004516 2.44e-05 1194 -18.4748575 0.0000000 3
AFR method Eagle - SHAPEIT 0 -0.0014466 2.44e-05 1194 -59.1868040 0.0000000 3
AMR method Beagle - Eagle 0 0.0005918 2.96e-05 1194 19.9906523 0.0000000 3
AMR method Beagle - SHAPEIT 0 -0.0005198 2.96e-05 1194 -17.5587685 0.0000000 3
AMR method Eagle - SHAPEIT 0 -0.0011117 2.96e-05 1194 -37.5494207 0.0000000 3
EAS method Beagle - Eagle 0 0.0006620 4.08e-05 1194 16.2104761 0.0000000 3
EAS method Beagle - SHAPEIT 0 -0.0005101 4.08e-05 1194 -12.4908586 0.0000000 3
EAS method Eagle - SHAPEIT 0 -0.0011721 4.08e-05 1194 -28.7013347 0.0000000 3
EUR method Beagle - Eagle 0 0.0004726 3.35e-05 1194 14.1075643 0.0000000 3
EUR method Beagle - SHAPEIT 0 -0.0003646 3.35e-05 1194 -10.8842658 0.0000000 3
EUR method Eagle - SHAPEIT 0 -0.0008372 3.35e-05 1194 -24.9918301 0.0000000 3
SAS method Beagle - Eagle 0 0.0007816 3.76e-05 1194 20.7940464 0.0000000 3
SAS method Beagle - SHAPEIT 0 -0.0006314 3.76e-05 1194 -16.8001160 0.0000000 3
SAS method Eagle - SHAPEIT 0 -0.0014130 3.76e-05 1194 -37.5941624 0.0000000 3
AFR method Beagle - Eagle 0 0.0009142 2.52e-05 1194 36.2285157 0.0000000 4
AFR method Beagle - SHAPEIT 0 -0.0003938 2.52e-05 1194 -15.6048424 0.0000000 4
AFR method Eagle - SHAPEIT 0 -0.0013079 2.52e-05 1194 -51.8333581 0.0000000 4
AMR method Beagle - Eagle 0 0.0005299 3.06e-05 1194 17.3368943 0.0000000 4
AMR method Beagle - SHAPEIT 0 -0.0005104 3.06e-05 1194 -16.6995945 0.0000000 4
AMR method Eagle - SHAPEIT 0 -0.0010403 3.06e-05 1194 -34.0364888 0.0000000 4
EAS method Beagle - Eagle 0 0.0005373 4.22e-05 1194 12.7438226 0.0000000 4
EAS method Beagle - SHAPEIT 0 -0.0005674 4.22e-05 1194 -13.4574360 0.0000000 4
EAS method Eagle - SHAPEIT 0 -0.0011047 4.22e-05 1194 -26.2012585 0.0000000 4
EUR method Beagle - Eagle 0 0.0004620 3.46e-05 1194 13.3594147 0.0000000 4
EUR method Beagle - SHAPEIT 0 -0.0003554 3.46e-05 1194 -10.2758253 0.0000000 4
EUR method Eagle - SHAPEIT 0 -0.0008174 3.46e-05 1194 -23.6352400 0.0000000 4
SAS method Beagle - Eagle 0 0.0007459 3.88e-05 1194 19.2217748 0.0000000 4
SAS method Beagle - SHAPEIT 0 -0.0005272 3.88e-05 1194 -13.5866435 0.0000000 4
SAS method Eagle - SHAPEIT 0 -0.0012731 3.88e-05 1194 -32.8084183 0.0000000 4
AFR method Beagle - Eagle 0 0.0009939 2.60e-05 1194 38.1919929 0.0000000 5
AFR method Beagle - SHAPEIT 0 -0.0004369 2.60e-05 1194 -16.7895457 0.0000000 5
AFR method Eagle - SHAPEIT 0 -0.0014308 2.60e-05 1194 -54.9815386 0.0000000 5
AMR method Beagle - Eagle 0 0.0005264 3.15e-05 1194 16.6998560 0.0000000 5
AMR method Beagle - SHAPEIT 0 -0.0005608 3.15e-05 1194 -17.7900173 0.0000000 5
AMR method Eagle - SHAPEIT 0 -0.0010872 3.15e-05 1194 -34.4898733 0.0000000 5
EAS method Beagle - Eagle 0 0.0006602 4.35e-05 1194 15.1833345 0.0000000 5
EAS method Beagle - SHAPEIT 0 -0.0006254 4.35e-05 1194 -14.3823834 0.0000000 5
EAS method Eagle - SHAPEIT 0 -0.0012856 4.35e-05 1194 -29.5657179 0.0000000 5
EUR method Beagle - Eagle 0 0.0004922 3.57e-05 1194 13.8001126 0.0000000 5
EUR method Beagle - SHAPEIT 0 -0.0003560 3.57e-05 1194 -9.9820022 0.0000000 5
EUR method Eagle - SHAPEIT 0 -0.0008483 3.57e-05 1194 -23.7821148 0.0000000 5
SAS method Beagle - Eagle 0 0.0008086 4.00e-05 1194 20.2052594 0.0000000 5
SAS method Beagle - SHAPEIT 0 -0.0006180 4.00e-05 1194 -15.4439938 0.0000000 5
SAS method Eagle - SHAPEIT 0 -0.0014266 4.00e-05 1194 -35.6492532 0.0000000 5
AFR method Beagle - Eagle 0 0.0008863 2.31e-05 1194 38.3462428 0.0000000 6
AFR method Beagle - SHAPEIT 0 -0.0003968 2.31e-05 1194 -17.1692991 0.0000000 6
AFR method Eagle - SHAPEIT 0 -0.0012832 2.31e-05 1194 -55.5155419 0.0000000 6
AMR method Beagle - Eagle 0 0.0004764 2.80e-05 1194 17.0174981 0.0000000 6
AMR method Beagle - SHAPEIT 0 -0.0004563 2.80e-05 1194 -16.2991758 0.0000000 6
AMR method Eagle - SHAPEIT 0 -0.0009328 2.80e-05 1194 -33.3166740 0.0000000 6
EAS method Beagle - Eagle 0 0.0006098 3.86e-05 1194 15.7914101 0.0000000 6
EAS method Beagle - SHAPEIT 0 -0.0004639 3.86e-05 1194 -12.0122281 0.0000000 6
EAS method Eagle - SHAPEIT 0 -0.0010737 3.86e-05 1194 -27.8036382 0.0000000 6
EUR method Beagle - Eagle 0 0.0004486 3.17e-05 1194 14.1608269 0.0000000 6
EUR method Beagle - SHAPEIT 0 -0.0003083 3.17e-05 1194 -9.7326504 0.0000000 6
EUR method Eagle - SHAPEIT 0 -0.0007569 3.17e-05 1194 -23.8934773 0.0000000 6
SAS method Beagle - Eagle 0 0.0007196 3.55e-05 1194 20.2457655 0.0000000 6
SAS method Beagle - SHAPEIT 0 -0.0005344 3.55e-05 1194 -15.0363649 0.0000000 6
SAS method Eagle - SHAPEIT 0 -0.0012540 3.55e-05 1194 -35.2821303 0.0000000 6
AFR method Beagle - Eagle 0 0.0008938 2.69e-05 1194 33.2346534 0.0000000 7
AFR method Beagle - SHAPEIT 0 -0.0005032 2.69e-05 1194 -18.7094220 0.0000000 7
AFR method Eagle - SHAPEIT 0 -0.0013969 2.69e-05 1194 -51.9440755 0.0000000 7
AMR method Beagle - Eagle 0 0.0005815 3.26e-05 1194 17.8518350 0.0000000 7
AMR method Beagle - SHAPEIT 0 -0.0004904 3.26e-05 1194 -15.0550500 0.0000000 7
AMR method Eagle - SHAPEIT 0 -0.0010719 3.26e-05 1194 -32.9068849 0.0000000 7
EAS method Beagle - Eagle 0 0.0006870 4.49e-05 1194 15.2899737 0.0000000 7
EAS method Beagle - SHAPEIT 0 -0.0005133 4.49e-05 1194 -11.4239565 0.0000000 7
EAS method Eagle - SHAPEIT 0 -0.0012004 4.49e-05 1194 -26.7139302 0.0000000 7
EUR method Beagle - Eagle 0 0.0004524 3.69e-05 1194 12.2724546 0.0000000 7
EUR method Beagle - SHAPEIT 0 -0.0003840 3.69e-05 1194 -10.4192855 0.0000000 7
EUR method Eagle - SHAPEIT 0 -0.0008364 3.69e-05 1194 -22.6917401 0.0000000 7
SAS method Beagle - Eagle 0 0.0007833 4.14e-05 1194 18.9413622 0.0000000 7
SAS method Beagle - SHAPEIT 0 -0.0006436 4.14e-05 1194 -15.5630446 0.0000000 7
SAS method Eagle - SHAPEIT 0 -0.0014269 4.14e-05 1194 -34.5044068 0.0000000 7
AFR method Beagle - Eagle 0 0.0010102 3.08e-05 1194 32.8076986 0.0000000 8
AFR method Beagle - SHAPEIT 0 -0.0004951 3.08e-05 1194 -16.0769328 0.0000000 8
AFR method Eagle - SHAPEIT 0 -0.0015053 3.08e-05 1194 -48.8846314 0.0000000 8
AMR method Beagle - Eagle 0 0.0005199 3.73e-05 1194 13.9391027 0.0000000 8
AMR method Beagle - SHAPEIT 0 -0.0005939 3.73e-05 1194 -15.9235135 0.0000000 8
AMR method Eagle - SHAPEIT 0 -0.0011138 3.73e-05 1194 -29.8626162 0.0000000 8
EAS method Beagle - Eagle 0 0.0006985 5.14e-05 1194 13.5757631 0.0000000 8
EAS method Beagle - SHAPEIT 0 -0.0004364 5.14e-05 1194 -8.4815494 0.0000000 8
EAS method Eagle - SHAPEIT 0 -0.0011348 5.14e-05 1194 -22.0573125 0.0000000 8
EUR method Beagle - Eagle 0 0.0004753 4.22e-05 1194 11.2625084 0.0000000 8
EUR method Beagle - SHAPEIT 0 -0.0003626 4.22e-05 1194 -8.5912484 0.0000000 8
EUR method Eagle - SHAPEIT 0 -0.0008379 4.22e-05 1194 -19.8537569 0.0000000 8
SAS method Beagle - Eagle 0 0.0007679 4.74e-05 1194 16.2171959 0.0000000 8
SAS method Beagle - SHAPEIT 0 -0.0006506 4.74e-05 1194 -13.7388077 0.0000000 8
SAS method Eagle - SHAPEIT 0 -0.0014185 4.74e-05 1194 -29.9560036 0.0000000 8
AFR method Beagle - Eagle 0 0.0010093 2.90e-05 1194 34.8231128 0.0000000 9
AFR method Beagle - SHAPEIT 0 -0.0005144 2.90e-05 1194 -17.7462965 0.0000000 9
AFR method Eagle - SHAPEIT 0 -0.0015237 2.90e-05 1194 -52.5694093 0.0000000 9
AMR method Beagle - Eagle 0 0.0005949 3.51e-05 1194 16.9440156 0.0000000 9
AMR method Beagle - SHAPEIT 0 -0.0005796 3.51e-05 1194 -16.5105705 0.0000000 9
AMR method Eagle - SHAPEIT 0 -0.0011745 3.51e-05 1194 -33.4545861 0.0000000 9
EAS method Beagle - Eagle 0 0.0007375 4.84e-05 1194 15.2281265 0.0000000 9
EAS method Beagle - SHAPEIT 0 -0.0005346 4.84e-05 1194 -11.0390979 0.0000000 9
EAS method Eagle - SHAPEIT 0 -0.0012721 4.84e-05 1194 -26.2672245 0.0000000 9
EUR method Beagle - Eagle 0 0.0005257 3.97e-05 1194 13.2338941 0.0000000 9
EUR method Beagle - SHAPEIT 0 -0.0003380 3.97e-05 1194 -8.5076843 0.0000000 9
EUR method Eagle - SHAPEIT 0 -0.0008637 3.97e-05 1194 -21.7415784 0.0000000 9
SAS method Beagle - Eagle 0 0.0008345 4.46e-05 1194 18.7234833 0.0000000 9
SAS method Beagle - SHAPEIT 0 -0.0006681 4.46e-05 1194 -14.9905111 0.0000000 9
SAS method Eagle - SHAPEIT 0 -0.0015027 4.46e-05 1194 -33.7139944 0.0000000 9
AFR method Beagle - Eagle 0 0.0009361 2.73e-05 1194 34.3517583 0.0000000 10
AFR method Beagle - SHAPEIT 0 -0.0004540 2.73e-05 1194 -16.6621745 0.0000000 10
AFR method Eagle - SHAPEIT 0 -0.0013901 2.73e-05 1194 -51.0139328 0.0000000 10
AMR method Beagle - Eagle 0 0.0005421 3.30e-05 1194 16.4240841 0.0000000 10
AMR method Beagle - SHAPEIT 0 -0.0005065 3.30e-05 1194 -15.3439172 0.0000000 10
AMR method Eagle - SHAPEIT 0 -0.0010486 3.30e-05 1194 -31.7680013 0.0000000 10
EAS method Beagle - Eagle 0 0.0006121 4.55e-05 1194 13.4448458 0.0000000 10
EAS method Beagle - SHAPEIT 0 -0.0005552 4.55e-05 1194 -12.1934201 0.0000000 10
EAS method Eagle - SHAPEIT 0 -0.0011673 4.55e-05 1194 -25.6382660 0.0000000 10
EUR method Beagle - Eagle 0 0.0004820 3.73e-05 1194 12.9047204 0.0000000 10
EUR method Beagle - SHAPEIT 0 -0.0003389 3.73e-05 1194 -9.0728078 0.0000000 10
EUR method Eagle - SHAPEIT 0 -0.0008208 3.73e-05 1194 -21.9775282 0.0000000 10
SAS method Beagle - Eagle 0 0.0006988 4.19e-05 1194 16.6755787 0.0000000 10
SAS method Beagle - SHAPEIT 0 -0.0006227 4.19e-05 1194 -14.8589263 0.0000000 10
SAS method Eagle - SHAPEIT 0 -0.0013214 4.19e-05 1194 -31.5345050 0.0000000 10
AFR method Beagle - Eagle 0 0.0009588 2.91e-05 1194 32.9384553 0.0000000 11
AFR method Beagle - SHAPEIT 0 -0.0004442 2.91e-05 1194 -15.2588026 0.0000000 11
AFR method Eagle - SHAPEIT 0 -0.0014030 2.91e-05 1194 -48.1972579 0.0000000 11
AMR method Beagle - Eagle 0 0.0005846 3.53e-05 1194 16.5804633 0.0000000 11
AMR method Beagle - SHAPEIT 0 -0.0004818 3.53e-05 1194 -13.6655230 0.0000000 11
AMR method Eagle - SHAPEIT 0 -0.0010664 3.53e-05 1194 -30.2459863 0.0000000 11
EAS method Beagle - Eagle 0 0.0006792 4.86e-05 1194 13.9649322 0.0000000 11
EAS method Beagle - SHAPEIT 0 -0.0005654 4.86e-05 1194 -11.6244214 0.0000000 11
EAS method Eagle - SHAPEIT 0 -0.0012445 4.86e-05 1194 -25.5893536 0.0000000 11
EUR method Beagle - Eagle 0 0.0004581 3.99e-05 1194 11.4830061 0.0000000 11
EUR method Beagle - SHAPEIT 0 -0.0003449 3.99e-05 1194 -8.6454033 0.0000000 11
EUR method Eagle - SHAPEIT 0 -0.0008030 3.99e-05 1194 -20.1284095 0.0000000 11
SAS method Beagle - Eagle 0 0.0007981 4.48e-05 1194 17.8298992 0.0000000 11
SAS method Beagle - SHAPEIT 0 -0.0005758 4.48e-05 1194 -12.8646792 0.0000000 11
SAS method Eagle - SHAPEIT 0 -0.0013739 4.48e-05 1194 -30.6945783 0.0000000 11
AFR method Beagle - Eagle 0 0.0009805 2.94e-05 1194 33.3456546 0.0000000 12
AFR method Beagle - SHAPEIT 0 -0.0004469 2.94e-05 1194 -15.1973596 0.0000000 12
AFR method Eagle - SHAPEIT 0 -0.0014273 2.94e-05 1194 -48.5430142 0.0000000 12
AMR method Beagle - Eagle 0 0.0005527 3.56e-05 1194 15.5188460 0.0000000 12
AMR method Beagle - SHAPEIT 0 -0.0005160 3.56e-05 1194 -14.4882119 0.0000000 12
AMR method Eagle - SHAPEIT 0 -0.0010687 3.56e-05 1194 -30.0070579 0.0000000 12
EAS method Beagle - Eagle 0 0.0006446 4.91e-05 1194 13.1209540 0.0000000 12
EAS method Beagle - SHAPEIT 0 -0.0005542 4.91e-05 1194 -11.2813808 0.0000000 12
EAS method Eagle - SHAPEIT 0 -0.0011989 4.91e-05 1194 -24.4023348 0.0000000 12
EUR method Beagle - Eagle 0 0.0004945 4.03e-05 1194 12.2707447 0.0000000 12
EUR method Beagle - SHAPEIT 0 -0.0003928 4.03e-05 1194 -9.7460039 0.0000000 12
EUR method Eagle - SHAPEIT 0 -0.0008873 4.03e-05 1194 -22.0167485 0.0000000 12
SAS method Beagle - Eagle 0 0.0008702 4.52e-05 1194 19.2460888 0.0000000 12
SAS method Beagle - SHAPEIT 0 -0.0006976 4.52e-05 1194 -15.4274222 0.0000000 12
SAS method Eagle - SHAPEIT 0 -0.0015678 4.52e-05 1194 -34.6735111 0.0000000 12
AFR method Beagle - Eagle 0 0.0009494 3.37e-05 1194 28.1796848 0.0000000 13
AFR method Beagle - SHAPEIT 0 -0.0004423 3.37e-05 1194 -13.1289115 0.0000000 13
AFR method Eagle - SHAPEIT 0 -0.0013918 3.37e-05 1194 -41.3085963 0.0000000 13
AMR method Beagle - Eagle 0 0.0006155 4.08e-05 1194 15.0829186 0.0000000 13
AMR method Beagle - SHAPEIT 0 -0.0005177 4.08e-05 1194 -12.6859367 0.0000000 13
AMR method Eagle - SHAPEIT 0 -0.0011332 4.08e-05 1194 -27.7688553 0.0000000 13
EAS method Beagle - Eagle 0 0.0006017 5.63e-05 1194 10.6882067 0.0000000 13
EAS method Beagle - SHAPEIT 0 -0.0005137 5.63e-05 1194 -9.1248408 0.0000000 13
EAS method Eagle - SHAPEIT 0 -0.0011153 5.63e-05 1194 -19.8130475 0.0000000 13
EUR method Beagle - Eagle 0 0.0005105 4.62e-05 1194 11.0549581 0.0000000 13
EUR method Beagle - SHAPEIT 0 -0.0003295 4.62e-05 1194 -7.1348827 0.0000000 13
EUR method Eagle - SHAPEIT 0 -0.0008400 4.62e-05 1194 -18.1898408 0.0000000 13
SAS method Beagle - Eagle 0 0.0005706 5.18e-05 1194 11.0132829 0.0000000 13
SAS method Beagle - SHAPEIT 0 -0.0006886 5.18e-05 1194 -13.2912596 0.0000000 13
SAS method Eagle - SHAPEIT 0 -0.0012592 5.18e-05 1194 -24.3045425 0.0000000 13
AFR method Beagle - Eagle 0 0.0009366 3.23e-05 1194 29.0277377 0.0000000 14
AFR method Beagle - SHAPEIT 0 -0.0004754 3.23e-05 1194 -14.7358601 0.0000000 14
AFR method Eagle - SHAPEIT 0 -0.0014120 3.23e-05 1194 -43.7635978 0.0000000 14
AMR method Beagle - Eagle 0 0.0006184 3.91e-05 1194 15.8231990 0.0000000 14
AMR method Beagle - SHAPEIT 0 -0.0005319 3.91e-05 1194 -13.6113316 0.0000000 14
AMR method Eagle - SHAPEIT 0 -0.0011503 3.91e-05 1194 -29.4345306 0.0000000 14
EAS method Beagle - Eagle 0 0.0005311 5.39e-05 1194 9.8515468 0.0000000 14
EAS method Beagle - SHAPEIT 0 -0.0006087 5.39e-05 1194 -11.2908917 0.0000000 14
EAS method Eagle - SHAPEIT 0 -0.0011398 5.39e-05 1194 -21.1424385 0.0000000 14
EUR method Beagle - Eagle 0 0.0004178 4.42e-05 1194 9.4470466 0.0000000 14
EUR method Beagle - SHAPEIT 0 -0.0004479 4.42e-05 1194 -10.1290810 0.0000000 14
EUR method Eagle - SHAPEIT 0 -0.0008657 4.42e-05 1194 -19.5761276 0.0000000 14
SAS method Beagle - Eagle 0 0.0007671 4.96e-05 1194 15.4608902 0.0000000 14
SAS method Beagle - SHAPEIT 0 -0.0006599 4.96e-05 1194 -13.2999178 0.0000000 14
SAS method Eagle - SHAPEIT 0 -0.0014270 4.96e-05 1194 -28.7608080 0.0000000 14
AFR method Beagle - Eagle 0 0.0009330 3.37e-05 1194 27.7137999 0.0000000 15
AFR method Beagle - SHAPEIT 0 -0.0004976 3.37e-05 1194 -14.7796766 0.0000000 15
AFR method Eagle - SHAPEIT 0 -0.0014306 3.37e-05 1194 -42.4934765 0.0000000 15
AMR method Beagle - Eagle 0 0.0006078 4.08e-05 1194 14.9045348 0.0000000 15
AMR method Beagle - SHAPEIT 0 -0.0005884 4.08e-05 1194 -14.4299566 0.0000000 15
AMR method Eagle - SHAPEIT 0 -0.0011962 4.08e-05 1194 -29.3344915 0.0000000 15
EAS method Beagle - Eagle 0 0.0006875 5.63e-05 1194 12.2219924 0.0000000 15
EAS method Beagle - SHAPEIT 0 -0.0006197 5.63e-05 1194 -11.0173355 0.0000000 15
EAS method Eagle - SHAPEIT 0 -0.0013072 5.63e-05 1194 -23.2393278 0.0000000 15
EUR method Beagle - Eagle 0 0.0004948 4.61e-05 1194 10.7222326 0.0000000 15
EUR method Beagle - SHAPEIT 0 -0.0004012 4.61e-05 1194 -8.6953236 0.0000000 15
EUR method Eagle - SHAPEIT 0 -0.0008960 4.61e-05 1194 -19.4175562 0.0000000 15
SAS method Beagle - Eagle 0 0.0007174 5.18e-05 1194 13.8571011 0.0000000 15
SAS method Beagle - SHAPEIT 0 -0.0007714 5.18e-05 1194 -14.9000610 0.0000000 15
SAS method Eagle - SHAPEIT 0 -0.0014888 5.18e-05 1194 -28.7571621 0.0000000 15
AFR method Beagle - Eagle 0 0.0010336 3.98e-05 1194 25.9845228 0.0000000 16
AFR method Beagle - SHAPEIT 0 -0.0005083 3.98e-05 1194 -12.7796384 0.0000000 16
AFR method Eagle - SHAPEIT 0 -0.0015419 3.98e-05 1194 -38.7641612 0.0000000 16
AMR method Beagle - Eagle 0 0.0007562 4.82e-05 1194 15.6958664 0.0000000 16
AMR method Beagle - SHAPEIT 0 -0.0005972 4.82e-05 1194 -12.3948802 0.0000000 16
AMR method Eagle - SHAPEIT 0 -0.0013534 4.82e-05 1194 -28.0907466 0.0000000 16
EAS method Beagle - Eagle 0 0.0008779 6.65e-05 1194 13.2097841 0.0000000 16
EAS method Beagle - SHAPEIT 0 -0.0005257 6.65e-05 1194 -7.9102447 0.0000000 16
EAS method Eagle - SHAPEIT 0 -0.0014036 6.65e-05 1194 -21.1200288 0.0000000 16
EUR method Beagle - Eagle 0 0.0004868 5.45e-05 1194 8.9291526 0.0000000 16
EUR method Beagle - SHAPEIT 0 -0.0005622 5.45e-05 1194 -10.3117112 0.0000000 16
EUR method Eagle - SHAPEIT 0 -0.0010490 5.45e-05 1194 -19.2408638 0.0000000 16
SAS method Beagle - Eagle 0 0.0011418 6.12e-05 1194 18.6669233 0.0000000 16
SAS method Beagle - SHAPEIT 0 -0.0005952 6.12e-05 1194 -9.7305849 0.0000000 16
SAS method Eagle - SHAPEIT 0 -0.0017370 6.12e-05 1194 -28.3975082 0.0000000 16
AFR method Beagle - Eagle 0 0.0009037 3.79e-05 1194 23.8142970 0.0000000 17
AFR method Beagle - SHAPEIT 0 -0.0005704 3.79e-05 1194 -15.0312054 0.0000000 17
AFR method Eagle - SHAPEIT 0 -0.0014741 3.79e-05 1194 -38.8455023 0.0000000 17
AMR method Beagle - Eagle 0 0.0006554 4.60e-05 1194 14.2596925 0.0000000 17
AMR method Beagle - SHAPEIT 0 -0.0005576 4.60e-05 1194 -12.1300782 0.0000000 17
AMR method Eagle - SHAPEIT 0 -0.0012130 4.60e-05 1194 -26.3897707 0.0000000 17
EAS method Beagle - Eagle 0 0.0007784 6.34e-05 1194 12.2766615 0.0000000 17
EAS method Beagle - SHAPEIT 0 -0.0004861 6.34e-05 1194 -7.6671341 0.0000000 17
EAS method Eagle - SHAPEIT 0 -0.0012645 6.34e-05 1194 -19.9437956 0.0000000 17
EUR method Beagle - Eagle 0 0.0005344 5.20e-05 1194 10.2753905 0.0000000 17
EUR method Beagle - SHAPEIT 0 -0.0004193 5.20e-05 1194 -8.0618827 0.0000000 17
EUR method Eagle - SHAPEIT 0 -0.0009537 5.20e-05 1194 -18.3372732 0.0000000 17
SAS method Beagle - Eagle 0 0.0007848 5.84e-05 1194 13.4487008 0.0000000 17
SAS method Beagle - SHAPEIT 0 -0.0007282 5.84e-05 1194 -12.4784645 0.0000000 17
SAS method Eagle - SHAPEIT 0 -0.0015130 5.84e-05 1194 -25.9271653 0.0000000 17
AFR method Beagle - Eagle 0 0.0009311 3.27e-05 1194 28.4332267 0.0000000 18
AFR method Beagle - SHAPEIT 0 -0.0005011 3.27e-05 1194 -15.3030643 0.0000000 18
AFR method Eagle - SHAPEIT 0 -0.0014322 3.27e-05 1194 -43.7362910 0.0000000 18
AMR method Beagle - Eagle 0 0.0006152 3.97e-05 1194 15.5104234 0.0000000 18
AMR method Beagle - SHAPEIT 0 -0.0005582 3.97e-05 1194 -14.0743641 0.0000000 18
AMR method Eagle - SHAPEIT 0 -0.0011735 3.97e-05 1194 -29.5847874 0.0000000 18
EAS method Beagle - Eagle 0 0.0006572 5.47e-05 1194 12.0110972 0.0000000 18
EAS method Beagle - SHAPEIT 0 -0.0004812 5.47e-05 1194 -8.7954706 0.0000000 18
EAS method Eagle - SHAPEIT 0 -0.0011384 5.47e-05 1194 -20.8065678 0.0000000 18
EUR method Beagle - Eagle 0 0.0004612 4.49e-05 1194 10.2768356 0.0000000 18
EUR method Beagle - SHAPEIT 0 -0.0003517 4.49e-05 1194 -7.8361100 0.0000000 18
EUR method Eagle - SHAPEIT 0 -0.0008129 4.49e-05 1194 -18.1129456 0.0000000 18
SAS method Beagle - Eagle 0 0.0008077 5.04e-05 1194 16.0393063 0.0000000 18
SAS method Beagle - SHAPEIT 0 -0.0006238 5.04e-05 1194 -12.3879880 0.0000000 18
SAS method Eagle - SHAPEIT 0 -0.0014315 5.04e-05 1194 -28.4272943 0.0000000 18
AFR method Beagle - Eagle 0 0.0009500 3.77e-05 1194 25.1730555 0.0000000 19
AFR method Beagle - SHAPEIT 0 -0.0004197 3.77e-05 1194 -11.1219244 0.0000000 19
AFR method Eagle - SHAPEIT 0 -0.0013697 3.77e-05 1194 -36.2949798 0.0000000 19
AMR method Beagle - Eagle 0 0.0005645 4.57e-05 1194 12.3499532 0.0000000 19
AMR method Beagle - SHAPEIT 0 -0.0004922 4.57e-05 1194 -10.7689680 0.0000000 19
AMR method Eagle - SHAPEIT 0 -0.0010567 4.57e-05 1194 -23.1189212 0.0000000 19
EAS method Beagle - Eagle 0 0.0007675 6.31e-05 1194 12.1723495 0.0000000 19
EAS method Beagle - SHAPEIT 0 -0.0005041 6.31e-05 1194 -7.9943179 0.0000000 19
EAS method Eagle - SHAPEIT 0 -0.0012715 6.31e-05 1194 -20.1666674 0.0000000 19
EUR method Beagle - Eagle 0 0.0005255 5.17e-05 1194 10.1592207 0.0000000 19
EUR method Beagle - SHAPEIT 0 -0.0003221 5.17e-05 1194 -6.2279019 0.0000000 19
EUR method Eagle - SHAPEIT 0 -0.0008476 5.17e-05 1194 -16.3871226 0.0000000 19
SAS method Beagle - Eagle 0 0.0008199 5.80e-05 1194 14.1290024 0.0000000 19
SAS method Beagle - SHAPEIT 0 -0.0006057 5.80e-05 1194 -10.4371748 0.0000000 19
SAS method Eagle - SHAPEIT 0 -0.0014256 5.80e-05 1194 -24.5661771 0.0000000 19
AFR method Beagle - Eagle 0 0.0009503 3.76e-05 1194 25.2430068 0.0000000 20
AFR method Beagle - SHAPEIT 0 -0.0004275 3.76e-05 1194 -11.3546946 0.0000000 20
AFR method Eagle - SHAPEIT 0 -0.0013778 3.76e-05 1194 -36.5977015 0.0000000 20
AMR method Beagle - Eagle 0 0.0006303 4.56e-05 1194 13.8225493 0.0000000 20
AMR method Beagle - SHAPEIT 0 -0.0005541 4.56e-05 1194 -12.1503575 0.0000000 20
AMR method Eagle - SHAPEIT 0 -0.0011844 4.56e-05 1194 -25.9729068 0.0000000 20
EAS method Beagle - Eagle 0 0.0006016 6.29e-05 1194 9.5633759 0.0000000 20
EAS method Beagle - SHAPEIT 0 -0.0006022 6.29e-05 1194 -9.5734425 0.0000000 20
EAS method Eagle - SHAPEIT 0 -0.0012037 6.29e-05 1194 -19.1368184 0.0000000 20
EUR method Beagle - Eagle 0 0.0004010 5.16e-05 1194 7.7713077 0.0000000 20
EUR method Beagle - SHAPEIT 0 -0.0004030 5.16e-05 1194 -7.8097288 0.0000000 20
EUR method Eagle - SHAPEIT 0 -0.0008040 5.16e-05 1194 -15.5810365 0.0000000 20
SAS method Beagle - Eagle 0 0.0007963 5.79e-05 1194 13.7553409 0.0000000 20
SAS method Beagle - SHAPEIT 0 -0.0005950 5.79e-05 1194 -10.2781881 0.0000000 20
SAS method Eagle - SHAPEIT 0 -0.0013913 5.79e-05 1194 -24.0335290 0.0000000 20
AFR method Beagle - Eagle 0 0.0007936 4.27e-05 1194 18.6063616 0.0000000 21
AFR method Beagle - SHAPEIT 0 -0.0005259 4.27e-05 1194 -12.3286685 0.0000000 21
AFR method Eagle - SHAPEIT 0 -0.0013195 4.27e-05 1194 -30.9350301 0.0000000 21
AMR method Beagle - Eagle 0 0.0004138 5.17e-05 1194 8.0095312 0.0000000 21
AMR method Beagle - SHAPEIT 0 -0.0005427 5.17e-05 1194 -10.5038851 0.0000000 21
AMR method Eagle - SHAPEIT 0 -0.0009565 5.17e-05 1194 -18.5134163 0.0000000 21
EAS method Beagle - Eagle 0 0.0006084 7.13e-05 1194 8.5367065 0.0000000 21
EAS method Beagle - SHAPEIT 0 -0.0004902 7.13e-05 1194 -6.8790138 0.0000000 21
EAS method Eagle - SHAPEIT 0 -0.0010986 7.13e-05 1194 -15.4157203 0.0000000 21
EUR method Beagle - Eagle 0 0.0004332 5.85e-05 1194 7.4102562 0.0000000 21
EUR method Beagle - SHAPEIT 0 -0.0004457 5.85e-05 1194 -7.6247750 0.0000000 21
EUR method Eagle - SHAPEIT 0 -0.0008789 5.85e-05 1194 -15.0350312 0.0000000 21
SAS method Beagle - Eagle 0 0.0006113 6.56e-05 1194 9.3201362 0.0000000 21
SAS method Beagle - SHAPEIT 0 -0.0006490 6.56e-05 1194 -9.8951103 0.0000000 21
SAS method Eagle - SHAPEIT 0 -0.0012603 6.56e-05 1194 -19.2152465 0.0000000 21
AFR method Beagle - Eagle 0 0.0008486 4.65e-05 1194 18.2576111 0.0000000 22
AFR method Beagle - SHAPEIT 0 -0.0005283 4.65e-05 1194 -11.3668957 0.0000000 22
AFR method Eagle - SHAPEIT 0 -0.0013769 4.65e-05 1194 -29.6245069 0.0000000 22
AMR method Beagle - Eagle 0 0.0005098 5.63e-05 1194 9.0551190 0.0000000 22
AMR method Beagle - SHAPEIT 0 -0.0005420 5.63e-05 1194 -9.6277848 0.0000000 22
AMR method Eagle - SHAPEIT 0 -0.0010518 5.63e-05 1194 -18.6829039 0.0000000 22
EAS method Beagle - Eagle 0 0.0005407 7.77e-05 1194 6.9627479 0.0000000 22
EAS method Beagle - SHAPEIT 0 -0.0005423 7.77e-05 1194 -6.9832513 0.0000000 22
EAS method Eagle - SHAPEIT 0 -0.0010830 7.77e-05 1194 -13.9459992 0.0000000 22
EUR method Beagle - Eagle 0 0.0003903 6.37e-05 1194 6.1269545 0.0000000 22
EUR method Beagle - SHAPEIT 0 -0.0004136 6.37e-05 1194 -6.4927862 0.0000000 22
EUR method Eagle - SHAPEIT 0 -0.0008039 6.37e-05 1194 -12.6197407 0.0000000 22
SAS method Beagle - Eagle 0 0.0006218 7.15e-05 1194 8.7001914 0.0000000 22
SAS method Beagle - SHAPEIT 0 -0.0007412 7.15e-05 1194 -10.3710731 0.0000000 22
SAS method Eagle - SHAPEIT 0 -0.0013631 7.15e-05 1194 -19.0712645 0.0000000 22
AFR method Beagle - Eagle 0 0.0000090 1.32e-05 1990 0.6832970 0.7732702 23
AFR method Beagle - SHAPEIT 0 -0.0001865 1.32e-05 1990 -14.1689679 0.0000000 23
AFR method Eagle - SHAPEIT 0 -0.0001955 1.32e-05 1990 -14.8522649 0.0000000 23
AMR method Beagle - Eagle 0 0.0000208 1.32e-05 1990 1.5785688 0.2551503 23
AMR method Beagle - SHAPEIT 0 -0.0001695 1.32e-05 1990 -12.8743522 0.0000000 23
AMR method Eagle - SHAPEIT 0 -0.0001902 1.32e-05 1990 -14.4529210 0.0000000 23
EAS method Beagle - Eagle 0 0.0000128 1.32e-05 1990 0.9717229 0.5948612 23
EAS method Beagle - SHAPEIT 0 -0.0001560 1.32e-05 1990 -11.8509140 0.0000000 23
EAS method Eagle - SHAPEIT 0 -0.0001688 1.32e-05 1990 -12.8226369 0.0000000 23
EUR method Beagle - Eagle 0 0.0000119 1.32e-05 1990 0.9049559 0.6372251 23
EUR method Beagle - SHAPEIT 0 -0.0001806 1.32e-05 1990 -13.7242659 0.0000000 23
EUR method Eagle - SHAPEIT 0 -0.0001925 1.32e-05 1990 -14.6292218 0.0000000 23
SAS method Beagle - Eagle 0 -0.0000318 1.32e-05 1990 -2.4127848 0.0420849 23
SAS method Beagle - SHAPEIT 0 -0.0002085 1.32e-05 1990 -15.8443297 0.0000000 23
SAS method Eagle - SHAPEIT 0 -0.0001768 1.32e-05 1990 -13.4315449 0.0000000 23
df_pop_pop %>% knitr::kable()
method term contrast null.value estimate std.error df statistic adj.p.value chrom
Beagle SUPER AFR - AMR 0 -0.0007318 0.0001295 634.6203 -5.6529163 0.0000002 1
Beagle SUPER AFR - EAS 0 -0.0026433 0.0001605 634.6203 -16.4701971 0.0000000 1
Beagle SUPER AFR - EUR 0 -0.0005607 0.0001398 634.6203 -4.0098589 0.0006479 1
Beagle SUPER AFR - SAS 0 -0.0021981 0.0001512 634.6203 -14.5388504 0.0000000 1
Beagle SUPER AMR - EAS 0 -0.0019115 0.0001701 634.6203 -11.2381013 0.0000000 1
Beagle SUPER AMR - EUR 0 0.0001711 0.0001508 634.6203 1.1349456 0.7879365 1
Beagle SUPER AMR - SAS 0 -0.0014662 0.0001613 634.6203 -9.0878937 0.0000000 1
Beagle SUPER EAS - EUR 0 0.0020826 0.0001781 634.6203 11.6923806 0.0000000 1
Beagle SUPER EAS - SAS 0 0.0004453 0.0001872 634.6203 2.3790629 0.1223711 1
Beagle SUPER EUR - SAS 0 -0.0016373 0.0001698 634.6203 -9.6439472 0.0000000 1
Eagle SUPER AFR - AMR 0 -0.0011347 0.0001295 634.6203 -8.7646480 0.0000000 1
Eagle SUPER AFR - EAS 0 -0.0029467 0.0001605 634.6203 -18.3605031 0.0000000 1
Eagle SUPER AFR - EUR 0 -0.0010682 0.0001398 634.6203 -7.6386069 0.0000000 1
Eagle SUPER AFR - SAS 0 -0.0023939 0.0001512 634.6203 -15.8340793 0.0000000 1
Eagle SUPER AMR - EAS 0 -0.0018120 0.0001701 634.6203 -10.6533194 0.0000000 1
Eagle SUPER AMR - EUR 0 0.0000665 0.0001508 634.6203 0.4412002 0.9921352 1
Eagle SUPER AMR - SAS 0 -0.0012592 0.0001613 634.6203 -7.8047376 0.0000000 1
Eagle SUPER EAS - EUR 0 0.0018786 0.0001781 634.6203 10.5467618 0.0000000 1
Eagle SUPER EAS - SAS 0 0.0005528 0.0001872 634.6203 2.9537531 0.0268840 1
Eagle SUPER EUR - SAS 0 -0.0013257 0.0001698 634.6203 -7.8085548 0.0000000 1
SHAPEIT SUPER AFR - AMR 0 -0.0008525 0.0001295 634.6203 -6.5851335 0.0000000 1
SHAPEIT SUPER AFR - EAS 0 -0.0027171 0.0001605 634.6203 -16.9296343 0.0000000 1
SHAPEIT SUPER AFR - EUR 0 -0.0004786 0.0001398 634.6203 -3.4223401 0.0059368 1
SHAPEIT SUPER AFR - SAS 0 -0.0024242 0.0001512 634.6203 -16.0342603 0.0000000 1
SHAPEIT SUPER AMR - EAS 0 -0.0018646 0.0001701 634.6203 -10.9620792 0.0000000 1
SHAPEIT SUPER AMR - EUR 0 0.0003739 0.0001508 634.6203 2.4804295 0.0963581 1
SHAPEIT SUPER AMR - SAS 0 -0.0015716 0.0001613 634.6203 -9.7411719 0.0000000 1
SHAPEIT SUPER EAS - EUR 0 0.0022385 0.0001781 634.6203 12.5676089 0.0000000 1
SHAPEIT SUPER EAS - SAS 0 0.0002929 0.0001872 634.6203 1.5650529 0.5204822 1
SHAPEIT SUPER EUR - SAS 0 -0.0019456 0.0001698 634.6203 -11.4594888 0.0000000 1
Beagle SUPER AFR - AMR 0 -0.0009213 0.0001293 637.2694 -7.1226395 0.0000000 2
Beagle SUPER AFR - EAS 0 -0.0027566 0.0001604 637.2694 -17.1909150 0.0000000 2
Beagle SUPER AFR - EUR 0 -0.0004559 0.0001397 637.2694 -3.2629891 0.0101862 2
Beagle SUPER AFR - SAS 0 -0.0022843 0.0001511 637.2694 -15.1223637 0.0000000 2
Beagle SUPER AMR - EAS 0 -0.0018353 0.0001699 637.2694 -10.7995069 0.0000000 2
Beagle SUPER AMR - EUR 0 0.0004654 0.0001506 637.2694 3.0898106 0.0177665 2
Beagle SUPER AMR - SAS 0 -0.0013630 0.0001612 637.2694 -8.4553700 0.0000000 2
Beagle SUPER EAS - EUR 0 0.0023007 0.0001780 637.2694 12.9281400 0.0000000 2
Beagle SUPER EAS - SAS 0 0.0004723 0.0001870 637.2694 2.5257317 0.0862447 2
Beagle SUPER EUR - SAS 0 -0.0018284 0.0001696 637.2694 -10.7787067 0.0000000 2
Eagle SUPER AFR - AMR 0 -0.0012853 0.0001293 637.2694 -9.9369481 0.0000000 2
Eagle SUPER AFR - EAS 0 -0.0030943 0.0001604 637.2694 -19.2970026 0.0000000 2
Eagle SUPER AFR - EUR 0 -0.0009408 0.0001397 637.2694 -6.7334498 0.0000000 2
Eagle SUPER AFR - SAS 0 -0.0024193 0.0001511 637.2694 -16.0162249 0.0000000 2
Eagle SUPER AMR - EAS 0 -0.0018090 0.0001699 637.2694 -10.6447030 0.0000000 2
Eagle SUPER AMR - EUR 0 0.0003446 0.0001506 637.2694 2.2874798 0.1502244 2
Eagle SUPER AMR - SAS 0 -0.0011340 0.0001612 637.2694 -7.0347607 0.0000000 2
Eagle SUPER EAS - EUR 0 0.0021535 0.0001780 637.2694 12.1012202 0.0000000 2
Eagle SUPER EAS - SAS 0 0.0006750 0.0001870 637.2694 3.6096813 0.0030410 2
Eagle SUPER EUR - SAS 0 -0.0014786 0.0001696 637.2694 -8.7162740 0.0000000 2
SHAPEIT SUPER AFR - AMR 0 -0.0009785 0.0001293 637.2694 -7.5645959 0.0000000 2
SHAPEIT SUPER AFR - EAS 0 -0.0029484 0.0001604 637.2694 -18.3871557 0.0000000 2
SHAPEIT SUPER AFR - EUR 0 -0.0004042 0.0001397 637.2694 -2.8930653 0.0321198 2
SHAPEIT SUPER AFR - SAS 0 -0.0024738 0.0001511 637.2694 -16.3768429 0.0000000 2
SHAPEIT SUPER AMR - EAS 0 -0.0019700 0.0001699 637.2694 -11.5918520 0.0000000 2
SHAPEIT SUPER AMR - EUR 0 0.0005743 0.0001506 637.2694 3.8124594 0.0014166 2
SHAPEIT SUPER AMR - SAS 0 -0.0014953 0.0001612 637.2694 -9.2762684 0.0000000 2
SHAPEIT SUPER EAS - EUR 0 0.0025442 0.0001780 637.2694 14.2964339 0.0000000 2
SHAPEIT SUPER EAS - SAS 0 0.0004746 0.0001870 637.2694 2.5381662 0.0836247 2
SHAPEIT SUPER EUR - SAS 0 -0.0020696 0.0001696 637.2694 -12.2004839 0.0000000 2
Beagle SUPER AFR - AMR 0 -0.0007966 0.0001254 635.7836 -6.3515083 0.0000000 3
Beagle SUPER AFR - EAS 0 -0.0026264 0.0001555 635.7836 -16.8917081 0.0000000 3
Beagle SUPER AFR - EUR 0 -0.0005786 0.0001355 635.7836 -4.2707710 0.0002173 3
Beagle SUPER AFR - SAS 0 -0.0020990 0.0001465 635.7836 -14.3307780 0.0000000 3
Beagle SUPER AMR - EAS 0 -0.0018298 0.0001648 635.7836 -11.1041104 0.0000000 3
Beagle SUPER AMR - EUR 0 0.0002180 0.0001461 635.7836 1.4928364 0.5675191 3
Beagle SUPER AMR - SAS 0 -0.0013024 0.0001563 635.7836 -8.3323635 0.0000000 3
Beagle SUPER EAS - EUR 0 0.0020478 0.0001726 635.7836 11.8673446 0.0000000 3
Beagle SUPER EAS - SAS 0 0.0005274 0.0001813 635.7836 2.9085959 0.0307031 3
Beagle SUPER EUR - SAS 0 -0.0015204 0.0001645 635.7836 -9.2437650 0.0000000 3
Eagle SUPER AFR - AMR 0 -0.0011999 0.0001254 635.7836 -9.5666227 0.0000000 3
Eagle SUPER AFR - EAS 0 -0.0029595 0.0001555 635.7836 -19.0338487 0.0000000 3
Eagle SUPER AFR - EUR 0 -0.0011011 0.0001355 635.7836 -8.1274319 0.0000000 3
Eagle SUPER AFR - SAS 0 -0.0023125 0.0001465 635.7836 -15.7885370 0.0000000 3
Eagle SUPER AMR - EAS 0 -0.0017596 0.0001648 635.7836 -10.6782633 0.0000000 3
Eagle SUPER AMR - EUR 0 0.0000988 0.0001461 635.7836 0.6764657 0.9614685 3
Eagle SUPER AMR - SAS 0 -0.0011127 0.0001563 635.7836 -7.1185536 0.0000000 3
Eagle SUPER EAS - EUR 0 0.0018584 0.0001726 635.7836 10.7697101 0.0000000 3
Eagle SUPER EAS - SAS 0 0.0006469 0.0001813 635.7836 3.5679475 0.0035411 3
Eagle SUPER EUR - SAS 0 -0.0012115 0.0001645 635.7836 -7.3653855 0.0000000 3
SHAPEIT SUPER AFR - AMR 0 -0.0008649 0.0001254 635.7836 -6.8958807 0.0000000 3
SHAPEIT SUPER AFR - EAS 0 -0.0026849 0.0001555 635.7836 -17.2682319 0.0000000 3
SHAPEIT SUPER AFR - EUR 0 -0.0004916 0.0001355 635.7836 -3.6290189 0.0028329 3
SHAPEIT SUPER AFR - SAS 0 -0.0022789 0.0001465 635.7836 -15.5589179 0.0000000 3
SHAPEIT SUPER AMR - EAS 0 -0.0018200 0.0001648 635.7836 -11.0450509 0.0000000 3
SHAPEIT SUPER AMR - EUR 0 0.0003732 0.0001461 635.7836 2.5555705 0.0800688 3
SHAPEIT SUPER AMR - SAS 0 -0.0014140 0.0001563 635.7836 -9.0464011 0.0000000 3
SHAPEIT SUPER EAS - EUR 0 0.0021933 0.0001726 635.7836 12.7104415 0.0000000 3
SHAPEIT SUPER EAS - SAS 0 0.0004060 0.0001813 635.7836 2.2393857 0.1666180 3
SHAPEIT SUPER EUR - SAS 0 -0.0017873 0.0001645 635.7836 -10.8659754 0.0000000 3
Beagle SUPER AFR - AMR 0 -0.0009254 0.0001150 646.7191 -8.0490906 0.0000000 4
Beagle SUPER AFR - EAS 0 -0.0023588 0.0001425 646.7191 -16.5501304 0.0000000 4
Beagle SUPER AFR - EUR 0 -0.0005374 0.0001242 646.7191 -4.3278569 0.0001692 4
Beagle SUPER AFR - SAS 0 -0.0020837 0.0001343 646.7191 -15.5199665 0.0000000 4
Beagle SUPER AMR - EAS 0 -0.0014334 0.0001511 646.7191 -9.4897459 0.0000000 4
Beagle SUPER AMR - EUR 0 0.0003879 0.0001339 646.7191 2.8976528 0.0316821 4
Beagle SUPER AMR - SAS 0 -0.0011583 0.0001433 646.7191 -8.0845605 0.0000000 4
Beagle SUPER EAS - EUR 0 0.0018214 0.0001582 646.7191 11.5147488 0.0000000 4
Beagle SUPER EAS - SAS 0 0.0002751 0.0001662 646.7191 1.6550659 0.4627529 4
Beagle SUPER EUR - SAS 0 -0.0015463 0.0001508 646.7191 -10.2557006 0.0000000 4
Eagle SUPER AFR - AMR 0 -0.0013097 0.0001150 646.7191 -11.3916004 0.0000000 4
Eagle SUPER AFR - EAS 0 -0.0027357 0.0001425 646.7191 -19.1944371 0.0000000 4
Eagle SUPER AFR - EUR 0 -0.0009896 0.0001242 646.7191 -7.9687864 0.0000000 4
Eagle SUPER AFR - SAS 0 -0.0022520 0.0001343 646.7191 -16.7735518 0.0000000 4
Eagle SUPER AMR - EAS 0 -0.0014260 0.0001511 646.7191 -9.4407604 0.0000000 4
Eagle SUPER AMR - EUR 0 0.0003201 0.0001339 646.7191 2.3907847 0.1190861 4
Eagle SUPER AMR - SAS 0 -0.0009424 0.0001433 646.7191 -6.5772043 0.0000000 4
Eagle SUPER EAS - EUR 0 0.0017461 0.0001582 646.7191 11.0389585 0.0000000 4
Eagle SUPER EAS - SAS 0 0.0004837 0.0001662 646.7191 2.9099644 0.0305661 4
Eagle SUPER EUR - SAS 0 -0.0012625 0.0001508 646.7191 -8.3731921 0.0000000 4
SHAPEIT SUPER AFR - AMR 0 -0.0010420 0.0001150 646.7191 -9.0637005 0.0000000 4
SHAPEIT SUPER AFR - EAS 0 -0.0025324 0.0001425 646.7191 -17.7682398 0.0000000 4
SHAPEIT SUPER AFR - EUR 0 -0.0004991 0.0001242 646.7191 -4.0188066 0.0006235 4
SHAPEIT SUPER AFR - SAS 0 -0.0022172 0.0001343 646.7191 -16.5138367 0.0000000 4
SHAPEIT SUPER AMR - EAS 0 -0.0014904 0.0001511 646.7191 -9.8668672 0.0000000 4
SHAPEIT SUPER AMR - EUR 0 0.0005430 0.0001339 646.7191 4.0555932 0.0005364 4
SHAPEIT SUPER AMR - SAS 0 -0.0011751 0.0001433 646.7191 -8.2017520 0.0000000 4
SHAPEIT SUPER EAS - EUR 0 0.0020334 0.0001582 646.7191 12.8549567 0.0000000 4
SHAPEIT SUPER EAS - SAS 0 0.0003153 0.0001662 646.7191 1.8967721 0.3200442 4
SHAPEIT SUPER EUR - SAS 0 -0.0017181 0.0001508 646.7191 -11.3952718 0.0000000 4
Beagle SUPER AFR - AMR 0 -0.0006740 0.0001304 637.7817 -5.1704390 0.0000031 5
Beagle SUPER AFR - EAS 0 -0.0025078 0.0001616 637.7817 -15.5185523 0.0000000 5
Beagle SUPER AFR - EUR 0 -0.0004742 0.0001408 637.7817 -3.3680775 0.0071550 5
Beagle SUPER AFR - SAS 0 -0.0021772 0.0001522 637.7817 -14.3018027 0.0000000 5
Beagle SUPER AMR - EAS 0 -0.0018338 0.0001713 637.7817 -10.7073889 0.0000000 5
Beagle SUPER AMR - EUR 0 0.0001998 0.0001518 637.7817 1.3159190 0.6814036 5
Beagle SUPER AMR - SAS 0 -0.0015032 0.0001625 637.7817 -9.2529070 0.0000000 5
Beagle SUPER EAS - EUR 0 0.0020336 0.0001793 637.7817 11.3387550 0.0000000 5
Beagle SUPER EAS - SAS 0 0.0003306 0.0001885 637.7817 1.7544970 0.4013676 5
Beagle SUPER EUR - SAS 0 -0.0017029 0.0001710 637.7817 -9.9614553 0.0000000 5
Eagle SUPER AFR - AMR 0 -0.0011415 0.0001304 637.7817 -8.7568075 0.0000000 5
Eagle SUPER AFR - EAS 0 -0.0028415 0.0001616 637.7817 -17.5836014 0.0000000 5
Eagle SUPER AFR - EUR 0 -0.0009759 0.0001408 637.7817 -6.9311149 0.0000000 5
Eagle SUPER AFR - SAS 0 -0.0023625 0.0001522 637.7817 -15.5191769 0.0000000 5
Eagle SUPER AMR - EAS 0 -0.0017000 0.0001713 637.7817 -9.9262320 0.0000000 5
Eagle SUPER AMR - EUR 0 0.0001656 0.0001518 637.7817 1.0907097 0.8113679 5
Eagle SUPER AMR - SAS 0 -0.0012210 0.0001625 637.7817 -7.5159454 0.0000000 5
Eagle SUPER EAS - EUR 0 0.0018656 0.0001793 637.7817 10.4021768 0.0000000 5
Eagle SUPER EAS - SAS 0 0.0004790 0.0001885 637.7817 2.5419231 0.0828449 5
Eagle SUPER EUR - SAS 0 -0.0013866 0.0001710 637.7817 -8.1108562 0.0000000 5
SHAPEIT SUPER AFR - AMR 0 -0.0007978 0.0001304 637.7817 -6.1204913 0.0000000 5
SHAPEIT SUPER AFR - EAS 0 -0.0026962 0.0001616 637.7817 -16.6846301 0.0000000 5
SHAPEIT SUPER AFR - EUR 0 -0.0003933 0.0001408 637.7817 -2.7935710 0.0426224 5
SHAPEIT SUPER AFR - SAS 0 -0.0023583 0.0001522 637.7817 -15.4915609 0.0000000 5
SHAPEIT SUPER AMR - EAS 0 -0.0018984 0.0001713 637.7817 -11.0845512 0.0000000 5
SHAPEIT SUPER AMR - EUR 0 0.0004045 0.0001518 637.7817 2.6646487 0.0604675 5
SHAPEIT SUPER AMR - SAS 0 -0.0015605 0.0001625 637.7817 -9.6054592 0.0000000 5
SHAPEIT SUPER EAS - EUR 0 0.0023029 0.0001793 637.7817 12.8404856 0.0000000 5
SHAPEIT SUPER EAS - SAS 0 0.0003380 0.0001885 637.7817 1.7933476 0.3783077 5
SHAPEIT SUPER EUR - SAS 0 -0.0019649 0.0001710 637.7817 -11.4941014 0.0000000 5
Beagle SUPER AFR - AMR 0 -0.0006305 0.0001157 637.8403 -5.4492722 0.0000007 6
Beagle SUPER AFR - EAS 0 -0.0022255 0.0001434 637.8403 -15.5161836 0.0000000 6
Beagle SUPER AFR - EUR 0 -0.0003023 0.0001250 637.8403 -2.4193871 0.1114328 6
Beagle SUPER AFR - SAS 0 -0.0018604 0.0001351 637.8403 -13.7691065 0.0000000 6
Beagle SUPER AMR - EAS 0 -0.0015950 0.0001520 637.8403 -10.4929281 0.0000000 6
Beagle SUPER AMR - EUR 0 0.0003281 0.0001347 637.8403 2.4353303 0.1073266 6
Beagle SUPER AMR - SAS 0 -0.0012299 0.0001442 637.8403 -8.5300001 0.0000000 6
Beagle SUPER EAS - EUR 0 0.0019231 0.0001592 637.8403 12.0814238 0.0000000 6
Beagle SUPER EAS - SAS 0 0.0003651 0.0001673 637.8403 2.1827753 0.1875155 6
Beagle SUPER EUR - SAS 0 -0.0015580 0.0001517 637.8403 -10.2684747 0.0000000 6
Eagle SUPER AFR - AMR 0 -0.0010403 0.0001157 637.8403 -8.9920646 0.0000000 6
Eagle SUPER AFR - EAS 0 -0.0025019 0.0001434 637.8403 -17.4437864 0.0000000 6
Eagle SUPER AFR - EUR 0 -0.0007401 0.0001250 637.8403 -5.9219707 0.0000001 6
Eagle SUPER AFR - SAS 0 -0.0020271 0.0001351 637.8403 -15.0030516 0.0000000 6
Eagle SUPER AMR - EAS 0 -0.0014616 0.0001520 637.8403 -9.6152489 0.0000000 6
Eagle SUPER AMR - EUR 0 0.0003003 0.0001347 637.8403 2.2287756 0.1703975 6
Eagle SUPER AMR - SAS 0 -0.0009867 0.0001442 637.8403 -6.8435322 0.0000000 6
Eagle SUPER EAS - EUR 0 0.0017619 0.0001592 637.8403 11.0684612 0.0000000 6
Eagle SUPER EAS - SAS 0 0.0004748 0.0001673 637.8403 2.8389530 0.0375143 6
Eagle SUPER EUR - SAS 0 -0.0012870 0.0001517 637.8403 -8.4824239 0.0000000 6
SHAPEIT SUPER AFR - AMR 0 -0.0006899 0.0001157 637.8403 -5.9633534 0.0000000 6
SHAPEIT SUPER AFR - EAS 0 -0.0022925 0.0001434 637.8403 -15.9836923 0.0000000 6
SHAPEIT SUPER AFR - EUR 0 -0.0002138 0.0001250 637.8403 -1.7110384 0.4278191 6
SHAPEIT SUPER AFR - SAS 0 -0.0019980 0.0001351 637.8403 -14.7874880 0.0000000 6
SHAPEIT SUPER AMR - EAS 0 -0.0016026 0.0001520 637.8403 -10.5427738 0.0000000 6
SHAPEIT SUPER AMR - EUR 0 0.0004761 0.0001347 637.8403 3.5338250 0.0040039 6
SHAPEIT SUPER AMR - SAS 0 -0.0013080 0.0001442 637.8403 -9.0717867 0.0000000 6
SHAPEIT SUPER EAS - EUR 0 0.0020787 0.0001592 637.8403 13.0587868 0.0000000 6
SHAPEIT SUPER EAS - SAS 0 0.0002946 0.0001673 637.8403 1.7610282 0.3974503 6
SHAPEIT SUPER EUR - SAS 0 -0.0017841 0.0001517 637.8403 -11.7587502 0.0000000 6
Beagle SUPER AFR - AMR 0 -0.0007361 0.0001246 645.0304 -5.9092743 0.0000001 7
Beagle SUPER AFR - EAS 0 -0.0025845 0.0001544 645.0304 -16.7364847 0.0000000 7
Beagle SUPER AFR - EUR 0 -0.0003421 0.0001345 645.0304 -2.5422493 0.0827634 7
Beagle SUPER AFR - SAS 0 -0.0020941 0.0001455 645.0304 -14.3958150 0.0000000 7
Beagle SUPER AMR - EAS 0 -0.0018484 0.0001637 645.0304 -11.2942408 0.0000000 7
Beagle SUPER AMR - EUR 0 0.0003940 0.0001451 645.0304 2.7163864 0.0526590 7
Beagle SUPER AMR - SAS 0 -0.0013580 0.0001552 645.0304 -8.7481578 0.0000000 7
Beagle SUPER EAS - EUR 0 0.0022424 0.0001714 645.0304 13.0845182 0.0000000 7
Beagle SUPER EAS - SAS 0 0.0004903 0.0001801 645.0304 2.7229525 0.0517329 7
Beagle SUPER EUR - SAS 0 -0.0017521 0.0001634 645.0304 -10.7253549 0.0000000 7
Eagle SUPER AFR - AMR 0 -0.0010483 0.0001246 645.0304 -8.4161640 0.0000000 7
Eagle SUPER AFR - EAS 0 -0.0027912 0.0001544 645.0304 -18.0753326 0.0000000 7
Eagle SUPER AFR - EUR 0 -0.0007835 0.0001345 645.0304 -5.8230836 0.0000001 7
Eagle SUPER AFR - SAS 0 -0.0022046 0.0001455 645.0304 -15.1551609 0.0000000 7
Eagle SUPER AMR - EAS 0 -0.0017429 0.0001637 645.0304 -10.6494816 0.0000000 7
Eagle SUPER AMR - EUR 0 0.0002649 0.0001451 645.0304 1.8259556 0.3594153 7
Eagle SUPER AMR - SAS 0 -0.0011562 0.0001552 645.0304 -7.4481734 0.0000000 7
Eagle SUPER EAS - EUR 0 0.0020077 0.0001714 645.0304 11.7151505 0.0000000 7
Eagle SUPER EAS - SAS 0 0.0005866 0.0001801 645.0304 3.2576416 0.0103620 7
Eagle SUPER EUR - SAS 0 -0.0014211 0.0001634 645.0304 -8.6993220 0.0000000 7
SHAPEIT SUPER AFR - AMR 0 -0.0007233 0.0001246 645.0304 -5.8069757 0.0000001 7
SHAPEIT SUPER AFR - EAS 0 -0.0025946 0.0001544 645.0304 -16.8023228 0.0000000 7
SHAPEIT SUPER AFR - EUR 0 -0.0002229 0.0001345 645.0304 -1.6570107 0.4615261 7
SHAPEIT SUPER AFR - SAS 0 -0.0022346 0.0001455 645.0304 -15.3613727 0.0000000 7
SHAPEIT SUPER AMR - EAS 0 -0.0018713 0.0001637 645.0304 -11.4342247 0.0000000 7
SHAPEIT SUPER AMR - EUR 0 0.0005004 0.0001451 645.0304 3.4496526 0.0053924 7
SHAPEIT SUPER AMR - SAS 0 -0.0015112 0.0001552 645.0304 -9.7350310 0.0000000 7
SHAPEIT SUPER EAS - EUR 0 0.0023717 0.0001714 645.0304 13.8388298 0.0000000 7
SHAPEIT SUPER EAS - SAS 0 0.0003601 0.0001801 645.0304 1.9994366 0.2673763 7
SHAPEIT SUPER EUR - SAS 0 -0.0020116 0.0001634 645.0304 -12.3142848 0.0000000 7
Beagle SUPER AFR - AMR 0 -0.0009059 0.0001328 652.8377 -6.8225783 0.0000000 8
Beagle SUPER AFR - EAS 0 -0.0028274 0.0001646 652.8377 -17.1771221 0.0000000 8
Beagle SUPER AFR - EUR 0 -0.0005110 0.0001434 652.8377 -3.5628465 0.0036009 8
Beagle SUPER AFR - SAS 0 -0.0021225 0.0001551 652.8377 -13.6883188 0.0000000 8
Beagle SUPER AMR - EAS 0 -0.0019215 0.0001744 652.8377 -11.0148751 0.0000000 8
Beagle SUPER AMR - EUR 0 0.0003949 0.0001546 652.8377 2.5540025 0.0803515 8
Beagle SUPER AMR - SAS 0 -0.0012166 0.0001655 652.8377 -7.3523501 0.0000000 8
Beagle SUPER EAS - EUR 0 0.0023164 0.0001827 652.8377 12.6802982 0.0000000 8
Beagle SUPER EAS - SAS 0 0.0007049 0.0001920 652.8377 3.6723189 0.0024081 8
Beagle SUPER EUR - SAS 0 -0.0016115 0.0001741 652.8377 -9.2547385 0.0000000 8
Eagle SUPER AFR - AMR 0 -0.0013962 0.0001328 652.8377 -10.5155964 0.0000000 8
Eagle SUPER AFR - EAS 0 -0.0031391 0.0001646 652.8377 -19.0712514 0.0000000 8
Eagle SUPER AFR - EUR 0 -0.0010459 0.0001434 652.8377 -7.2926473 0.0000000 8
Eagle SUPER AFR - SAS 0 -0.0023648 0.0001551 652.8377 -15.2511374 0.0000000 8
Eagle SUPER AMR - EAS 0 -0.0017429 0.0001744 652.8377 -9.9912717 0.0000000 8
Eagle SUPER AMR - EUR 0 0.0003503 0.0001546 652.8377 2.2656932 0.1574626 8
Eagle SUPER AMR - SAS 0 -0.0009686 0.0001655 652.8377 -5.8535156 0.0000001 8
Eagle SUPER EAS - EUR 0 0.0020933 0.0001827 652.8377 11.4587892 0.0000000 8
Eagle SUPER EAS - SAS 0 0.0007744 0.0001920 652.8377 4.0341300 0.0005851 8
Eagle SUPER EUR - SAS 0 -0.0013189 0.0001741 652.8377 -7.5743995 0.0000000 8
SHAPEIT SUPER AFR - AMR 0 -0.0010047 0.0001328 652.8377 -7.5671741 0.0000000 8
SHAPEIT SUPER AFR - EAS 0 -0.0027687 0.0001646 652.8377 -16.8206078 0.0000000 8
SHAPEIT SUPER AFR - EUR 0 -0.0003785 0.0001434 652.8377 -2.6391939 0.0646155 8
SHAPEIT SUPER AFR - SAS 0 -0.0022780 0.0001551 652.8377 -14.6912134 0.0000000 8
SHAPEIT SUPER AMR - EAS 0 -0.0017640 0.0001744 652.8377 -10.1117547 0.0000000 8
SHAPEIT SUPER AMR - EUR 0 0.0006262 0.0001546 652.8377 4.0501547 0.0005479 8
SHAPEIT SUPER AMR - SAS 0 -0.0012732 0.0001655 652.8377 -7.6946586 0.0000000 8
SHAPEIT SUPER EAS - EUR 0 0.0023902 0.0001827 652.8377 13.0842075 0.0000000 8
SHAPEIT SUPER EAS - SAS 0 0.0004907 0.0001920 652.8377 2.5564680 0.0798559 8
SHAPEIT SUPER EUR - SAS 0 -0.0018995 0.0001741 652.8377 -10.9085553 0.0000000 8
Beagle SUPER AFR - AMR 0 -0.0005758 0.0001327 646.2063 -4.3390163 0.0001612 9
Beagle SUPER AFR - EAS 0 -0.0026399 0.0001645 646.2063 -16.0458333 0.0000000 9
Beagle SUPER AFR - EUR 0 -0.0003953 0.0001433 646.2063 -2.7573899 0.0470956 9
Beagle SUPER AFR - SAS 0 -0.0020545 0.0001550 646.2063 -13.2567412 0.0000000 9
Beagle SUPER AMR - EAS 0 -0.0020640 0.0001744 646.2063 -11.8377240 0.0000000 9
Beagle SUPER AMR - EUR 0 0.0001806 0.0001545 646.2063 1.1684006 0.7694431 9
Beagle SUPER AMR - SAS 0 -0.0014787 0.0001654 646.2063 -8.9407557 0.0000000 9
Beagle SUPER EAS - EUR 0 0.0022446 0.0001826 646.2063 12.2933033 0.0000000 9
Beagle SUPER EAS - SAS 0 0.0005853 0.0001919 646.2063 3.0508456 0.0200357 9
Beagle SUPER EUR - SAS 0 -0.0016593 0.0001740 646.2063 -9.5338297 0.0000000 9
Eagle SUPER AFR - AMR 0 -0.0009903 0.0001327 646.2063 -7.4620550 0.0000000 9
Eagle SUPER AFR - EAS 0 -0.0029117 0.0001645 646.2063 -17.6982554 0.0000000 9
Eagle SUPER AFR - EUR 0 -0.0008789 0.0001433 646.2063 -6.1310076 0.0000000 9
Eagle SUPER AFR - SAS 0 -0.0022293 0.0001550 646.2063 -14.3846208 0.0000000 9
Eagle SUPER AMR - EAS 0 -0.0019214 0.0001744 646.2063 -11.0198779 0.0000000 9
Eagle SUPER AMR - EUR 0 0.0001114 0.0001545 646.2063 0.7210139 0.9516534 9
Eagle SUPER AMR - SAS 0 -0.0012391 0.0001654 646.2063 -7.4917100 0.0000000 9
Eagle SUPER EAS - EUR 0 0.0020329 0.0001826 646.2063 11.1336385 0.0000000 9
Eagle SUPER EAS - SAS 0 0.0006824 0.0001919 646.2063 3.5567302 0.0036839 9
Eagle SUPER EUR - SAS 0 -0.0013505 0.0001740 646.2063 -7.7595503 0.0000000 9
SHAPEIT SUPER AFR - AMR 0 -0.0006411 0.0001327 646.2063 -4.8309266 0.0000168 9
SHAPEIT SUPER AFR - EAS 0 -0.0026601 0.0001645 646.2063 -16.1688267 0.0000000 9
SHAPEIT SUPER AFR - EUR 0 -0.0002189 0.0001433 646.2063 -1.5268710 0.5453062 9
SHAPEIT SUPER AFR - SAS 0 -0.0022083 0.0001550 646.2063 -14.2489629 0.0000000 9
SHAPEIT SUPER AMR - EAS 0 -0.0020190 0.0001744 646.2063 -11.5793729 0.0000000 9
SHAPEIT SUPER AMR - EUR 0 0.0004222 0.0001545 646.2063 2.7322012 0.0504498 9
SHAPEIT SUPER AMR - SAS 0 -0.0015672 0.0001654 646.2063 -9.4758191 0.0000000 9
SHAPEIT SUPER EAS - EUR 0 0.0024412 0.0001826 646.2063 13.3701893 0.0000000 9
SHAPEIT SUPER EAS - SAS 0 0.0004518 0.0001919 646.2063 2.3548023 0.1293093 9
SHAPEIT SUPER EUR - SAS 0 -0.0019894 0.0001740 646.2063 -11.4308893 0.0000000 9
Beagle SUPER AFR - AMR 0 -0.0006314 0.0001174 652.8895 -5.3760585 0.0000011 10
Beagle SUPER AFR - EAS 0 -0.0022866 0.0001456 652.8895 -15.7044124 0.0000000 10
Beagle SUPER AFR - EUR 0 -0.0002953 0.0001269 652.8895 -2.3280256 0.1373257 10
Beagle SUPER AFR - SAS 0 -0.0019328 0.0001372 652.8895 -14.0921578 0.0000000 10
Beagle SUPER AMR - EAS 0 -0.0016552 0.0001543 652.8895 -10.7262582 0.0000000 10
Beagle SUPER AMR - EUR 0 0.0003361 0.0001368 652.8895 2.4572029 0.1018566 10
Beagle SUPER AMR - SAS 0 -0.0013014 0.0001464 652.8895 -8.8914666 0.0000000 10
Beagle SUPER EAS - EUR 0 0.0019912 0.0001616 652.8895 12.3227540 0.0000000 10
Beagle SUPER EAS - SAS 0 0.0003537 0.0001698 652.8895 2.0832255 0.2285453 10
Beagle SUPER EUR - SAS 0 -0.0016375 0.0001540 652.8895 -10.6313957 0.0000000 10
Eagle SUPER AFR - AMR 0 -0.0010254 0.0001174 652.8895 -8.7305803 0.0000000 10
Eagle SUPER AFR - EAS 0 -0.0026105 0.0001456 652.8895 -17.9292957 0.0000000 10
Eagle SUPER AFR - EUR 0 -0.0007495 0.0001269 652.8895 -5.9076566 0.0000001 10
Eagle SUPER AFR - SAS 0 -0.0021702 0.0001372 652.8895 -15.8223888 0.0000000 10
Eagle SUPER AMR - EAS 0 -0.0015851 0.0001543 652.8895 -10.2723781 0.0000000 10
Eagle SUPER AMR - EUR 0 0.0002759 0.0001368 652.8895 2.0175080 0.2586651 10
Eagle SUPER AMR - SAS 0 -0.0011448 0.0001464 652.8895 -7.8211189 0.0000000 10
Eagle SUPER EAS - EUR 0 0.0018611 0.0001616 652.8895 11.5171669 0.0000000 10
Eagle SUPER EAS - SAS 0 0.0004403 0.0001698 652.8895 2.5934288 0.0727193 10
Eagle SUPER EUR - SAS 0 -0.0014207 0.0001540 652.8895 -9.2238204 0.0000000 10
SHAPEIT SUPER AFR - AMR 0 -0.0006838 0.0001174 652.8895 -5.8223057 0.0000001 10
SHAPEIT SUPER AFR - EAS 0 -0.0023877 0.0001456 652.8895 -16.3989433 0.0000000 10
SHAPEIT SUPER AFR - EUR 0 -0.0001801 0.0001269 652.8895 -1.4200295 0.6149264 10
SHAPEIT SUPER AFR - SAS 0 -0.0021015 0.0001372 652.8895 -15.3214358 0.0000000 10
SHAPEIT SUPER AMR - EAS 0 -0.0017039 0.0001543 652.8895 -11.0419432 0.0000000 10
SHAPEIT SUPER AMR - EUR 0 0.0005037 0.0001368 652.8895 3.6826315 0.0023171 10
SHAPEIT SUPER AMR - SAS 0 -0.0014176 0.0001464 652.8895 -9.6853067 0.0000000 10
SHAPEIT SUPER EAS - EUR 0 0.0022075 0.0001616 652.8895 13.6614154 0.0000000 10
SHAPEIT SUPER EAS - SAS 0 0.0002862 0.0001698 652.8895 1.6857926 0.4434519 10
SHAPEIT SUPER EUR - SAS 0 -0.0019213 0.0001540 652.8895 -12.4739082 0.0000000 10
Beagle SUPER AFR - AMR 0 -0.0008881 0.0001337 645.9162 -6.6449083 0.0000000 11
Beagle SUPER AFR - EAS 0 -0.0025694 0.0001657 645.9162 -15.5069028 0.0000000 11
Beagle SUPER AFR - EUR 0 -0.0004370 0.0001444 645.9162 -3.0272624 0.0215370 11
Beagle SUPER AFR - SAS 0 -0.0023209 0.0001561 645.9162 -14.8694553 0.0000000 11
Beagle SUPER AMR - EAS 0 -0.0016813 0.0001756 645.9162 -9.5741479 0.0000000 11
Beagle SUPER AMR - EUR 0 0.0004511 0.0001556 645.9162 2.8982188 0.0316311 11
Beagle SUPER AMR - SAS 0 -0.0014328 0.0001666 645.9162 -8.6017126 0.0000000 11
Beagle SUPER EAS - EUR 0 0.0021323 0.0001839 645.9162 11.5958272 0.0000000 11
Beagle SUPER EAS - SAS 0 0.0002485 0.0001932 645.9162 1.2859601 0.6999985 11
Beagle SUPER EUR - SAS 0 -0.0018839 0.0001753 645.9162 -10.7476491 0.0000000 11
Eagle SUPER AFR - AMR 0 -0.0012623 0.0001337 645.9162 -9.4446092 0.0000000 11
Eagle SUPER AFR - EAS 0 -0.0028490 0.0001657 645.9162 -17.1943653 0.0000000 11
Eagle SUPER AFR - EUR 0 -0.0009377 0.0001444 645.9162 -6.4952428 0.0000000 11
Eagle SUPER AFR - SAS 0 -0.0024816 0.0001561 645.9162 -15.8989505 0.0000000 11
Eagle SUPER AMR - EAS 0 -0.0015867 0.0001756 645.9162 -9.0354637 0.0000000 11
Eagle SUPER AMR - EUR 0 0.0003246 0.0001556 645.9162 2.0856446 0.2274959 11
Eagle SUPER AMR - SAS 0 -0.0012193 0.0001666 645.9162 -7.3199222 0.0000000 11
Eagle SUPER EAS - EUR 0 0.0019113 0.0001839 645.9162 10.3936527 0.0000000 11
Eagle SUPER EAS - SAS 0 0.0003674 0.0001932 645.9162 1.9013670 0.3175734 11
Eagle SUPER EUR - SAS 0 -0.0015439 0.0001753 645.9162 -8.8080393 0.0000000 11
SHAPEIT SUPER AFR - AMR 0 -0.0009258 0.0001337 645.9162 -6.9266630 0.0000000 11
SHAPEIT SUPER AFR - EAS 0 -0.0026906 0.0001657 645.9162 -16.2383552 0.0000000 11
SHAPEIT SUPER AFR - EUR 0 -0.0003378 0.0001444 645.9162 -2.3398088 0.1337613 11
SHAPEIT SUPER AFR - SAS 0 -0.0024526 0.0001561 645.9162 -15.7131379 0.0000000 11
SHAPEIT SUPER AMR - EAS 0 -0.0017648 0.0001756 645.9162 -10.0498693 0.0000000 11
SHAPEIT SUPER AMR - EUR 0 0.0005880 0.0001556 645.9162 3.7778259 0.0016169 11
SHAPEIT SUPER AMR - SAS 0 -0.0015268 0.0001666 645.9162 -9.1662151 0.0000000 11
SHAPEIT SUPER EAS - EUR 0 0.0023528 0.0001839 645.9162 12.7946120 0.0000000 11
SHAPEIT SUPER EAS - SAS 0 0.0002380 0.0001932 645.9162 1.2316703 0.7328459 11
SHAPEIT SUPER EUR - SAS 0 -0.0021148 0.0001753 645.9162 -12.0651479 0.0000000 11
Beagle SUPER AFR - AMR 0 -0.0007627 0.0001348 646.0960 -5.6592590 0.0000002 12
Beagle SUPER AFR - EAS 0 -0.0025199 0.0001671 646.0960 -15.0821499 0.0000000 12
Beagle SUPER AFR - EUR 0 -0.0004272 0.0001456 646.0960 -2.9342325 0.0284667 12
Beagle SUPER AFR - SAS 0 -0.0022723 0.0001574 646.0960 -14.4372952 0.0000000 12
Beagle SUPER AMR - EAS 0 -0.0017572 0.0001771 646.0960 -9.9235652 0.0000000 12
Beagle SUPER AMR - EUR 0 0.0003356 0.0001569 646.0960 2.1381019 0.2052420 12
Beagle SUPER AMR - SAS 0 -0.0015096 0.0001680 646.0960 -8.9876408 0.0000000 12
Beagle SUPER EAS - EUR 0 0.0020928 0.0001854 646.0960 11.2861403 0.0000000 12
Beagle SUPER EAS - SAS 0 0.0002476 0.0001948 646.0960 1.2708241 0.7092743 12
Beagle SUPER EUR - SAS 0 -0.0018452 0.0001768 646.0960 -10.4394404 0.0000000 12
Eagle SUPER AFR - AMR 0 -0.0011905 0.0001348 646.0960 -8.8332387 0.0000000 12
Eagle SUPER AFR - EAS 0 -0.0028558 0.0001671 646.0960 -17.0923896 0.0000000 12
Eagle SUPER AFR - EUR 0 -0.0009131 0.0001456 646.0960 -6.2724569 0.0000000 12
Eagle SUPER AFR - SAS 0 -0.0023826 0.0001574 646.0960 -15.1378204 0.0000000 12
Eagle SUPER AMR - EAS 0 -0.0016653 0.0001771 646.0960 -9.4045699 0.0000000 12
Eagle SUPER AMR - EUR 0 0.0002774 0.0001569 646.0960 1.7672893 0.3936989 12
Eagle SUPER AMR - SAS 0 -0.0011921 0.0001680 646.0960 -7.0972617 0.0000000 12
Eagle SUPER EAS - EUR 0 0.0019427 0.0001854 646.0960 10.4766736 0.0000000 12
Eagle SUPER EAS - SAS 0 0.0004732 0.0001948 646.0960 2.4287585 0.1089874 12
Eagle SUPER EUR - SAS 0 -0.0014695 0.0001768 646.0960 -8.3137598 0.0000000 12
SHAPEIT SUPER AFR - AMR 0 -0.0008319 0.0001348 646.0960 -6.1723147 0.0000000 12
SHAPEIT SUPER AFR - EAS 0 -0.0026273 0.0001671 646.0960 -15.7248272 0.0000000 12
SHAPEIT SUPER AFR - EUR 0 -0.0003731 0.0001456 646.0960 -2.5626655 0.0786338 12
SHAPEIT SUPER AFR - SAS 0 -0.0025230 0.0001574 646.0960 -16.0301577 0.0000000 12
SHAPEIT SUPER AMR - EAS 0 -0.0017954 0.0001771 646.0960 -10.1394739 0.0000000 12
SHAPEIT SUPER AMR - EUR 0 0.0004588 0.0001569 646.0960 2.9233301 0.0293942 12
SHAPEIT SUPER AMR - SAS 0 -0.0016912 0.0001680 646.0960 -10.0685750 0.0000000 12
SHAPEIT SUPER EAS - EUR 0 0.0022543 0.0001854 646.0960 12.1569363 0.0000000 12
SHAPEIT SUPER EAS - SAS 0 0.0001043 0.0001948 646.0960 0.5352240 0.9836739 12
SHAPEIT SUPER EUR - SAS 0 -0.0021500 0.0001768 646.0960 -12.1638958 0.0000000 12
Beagle SUPER AFR - AMR 0 -0.0006153 0.0001289 669.0456 -4.7743042 0.0000218 13
Beagle SUPER AFR - EAS 0 -0.0023526 0.0001598 669.0456 -14.7259570 0.0000000 13
Beagle SUPER AFR - EUR 0 -0.0004368 0.0001392 669.0456 -3.1382968 0.0152258 13
Beagle SUPER AFR - SAS 0 -0.0018945 0.0001505 669.0456 -12.5885369 0.0000000 13
Beagle SUPER AMR - EAS 0 -0.0017373 0.0001693 669.0456 -10.2610323 0.0000000 13
Beagle SUPER AMR - EUR 0 0.0001784 0.0001501 669.0456 1.1888814 0.7578176 13
Beagle SUPER AMR - SAS 0 -0.0012793 0.0001606 669.0456 -7.9653293 0.0000000 13
Beagle SUPER EAS - EUR 0 0.0019158 0.0001773 669.0456 10.8049849 0.0000000 13
Beagle SUPER EAS - SAS 0 0.0004581 0.0001863 669.0456 2.4588011 0.1014366 13
Beagle SUPER EUR - SAS 0 -0.0014577 0.0001690 669.0456 -8.6250750 0.0000000 13
Eagle SUPER AFR - AMR 0 -0.0009492 0.0001289 669.0456 -7.3652891 0.0000000 13
Eagle SUPER AFR - EAS 0 -0.0027004 0.0001598 669.0456 -16.9026822 0.0000000 13
Eagle SUPER AFR - EUR 0 -0.0008758 0.0001392 669.0456 -6.2916039 0.0000000 13
Eagle SUPER AFR - SAS 0 -0.0022733 0.0001505 669.0456 -15.1057387 0.0000000 13
Eagle SUPER AMR - EAS 0 -0.0017512 0.0001693 669.0456 -10.3428558 0.0000000 13
Eagle SUPER AMR - EUR 0 0.0000734 0.0001501 669.0456 0.4889550 0.9883788 13
Eagle SUPER AMR - SAS 0 -0.0013242 0.0001606 669.0456 -8.2450884 0.0000000 13
Eagle SUPER EAS - EUR 0 0.0018246 0.0001773 669.0456 10.2907058 0.0000000 13
Eagle SUPER EAS - SAS 0 0.0004270 0.0001863 669.0456 2.2919966 0.1486828 13
Eagle SUPER EUR - SAS 0 -0.0013976 0.0001690 669.0456 -8.2694214 0.0000000 13
SHAPEIT SUPER AFR - AMR 0 -0.0006906 0.0001289 669.0456 -5.3591698 0.0000011 13
SHAPEIT SUPER AFR - EAS 0 -0.0024239 0.0001598 669.0456 -15.1724421 0.0000000 13
SHAPEIT SUPER AFR - EUR 0 -0.0003240 0.0001392 669.0456 -2.3274686 0.1374642 13
SHAPEIT SUPER AFR - SAS 0 -0.0021408 0.0001505 669.0456 -14.2250141 0.0000000 13
SHAPEIT SUPER AMR - EAS 0 -0.0017333 0.0001693 669.0456 -10.2371656 0.0000000 13
SHAPEIT SUPER AMR - EUR 0 0.0003667 0.0001501 669.0456 2.4432167 0.1052775 13
SHAPEIT SUPER AMR - SAS 0 -0.0014502 0.0001606 669.0456 -9.0295128 0.0000000 13
SHAPEIT SUPER EAS - EUR 0 0.0021000 0.0001773 669.0456 11.8438597 0.0000000 13
SHAPEIT SUPER EAS - SAS 0 0.0002831 0.0001863 669.0456 1.5197310 0.5499473 13
SHAPEIT SUPER EUR - SAS 0 -0.0018168 0.0001690 669.0456 -10.7501608 0.0000000 13
Beagle SUPER AFR - AMR 0 -0.0009420 0.0001331 658.3266 -7.0779502 0.0000000 14
Beagle SUPER AFR - EAS 0 -0.0023472 0.0001650 658.3266 -14.2257571 0.0000000 14
Beagle SUPER AFR - EUR 0 -0.0003467 0.0001438 658.3266 -2.4118908 0.1133633 14
Beagle SUPER AFR - SAS 0 -0.0021230 0.0001554 658.3266 -13.6587651 0.0000000 14
Beagle SUPER AMR - EAS 0 -0.0014052 0.0001749 658.3266 -8.0357105 0.0000000 14
Beagle SUPER AMR - EUR 0 0.0005953 0.0001550 658.3266 3.8408804 0.0012650 14
Beagle SUPER AMR - SAS 0 -0.0011809 0.0001659 658.3266 -7.1197449 0.0000000 14
Beagle SUPER EAS - EUR 0 0.0020005 0.0001831 658.3266 10.9245709 0.0000000 14
Beagle SUPER EAS - SAS 0 0.0002242 0.0001924 658.3266 1.1653455 0.7711588 14
Beagle SUPER EUR - SAS 0 -0.0017762 0.0001745 658.3266 -10.1763917 0.0000000 14
Eagle SUPER AFR - AMR 0 -0.0012602 0.0001331 658.3266 -9.4686260 0.0000000 14
Eagle SUPER AFR - EAS 0 -0.0027527 0.0001650 658.3266 -16.6832941 0.0000000 14
Eagle SUPER AFR - EUR 0 -0.0008655 0.0001438 658.3266 -6.0206863 0.0000000 14
Eagle SUPER AFR - SAS 0 -0.0022924 0.0001554 658.3266 -14.7491179 0.0000000 14
Eagle SUPER AMR - EAS 0 -0.0014925 0.0001749 658.3266 -8.5349566 0.0000000 14
Eagle SUPER AMR - EUR 0 0.0003947 0.0001550 658.3266 2.5464490 0.0818751 14
Eagle SUPER AMR - SAS 0 -0.0010322 0.0001659 658.3266 -6.2231854 0.0000000 14
Eagle SUPER EAS - EUR 0 0.0018871 0.0001831 658.3266 10.3057198 0.0000000 14
Eagle SUPER EAS - SAS 0 0.0004602 0.0001924 658.3266 2.3919441 0.1187438 14
Eagle SUPER EUR - SAS 0 -0.0014269 0.0001745 658.3266 -8.1749940 0.0000000 14
SHAPEIT SUPER AFR - AMR 0 -0.0009985 0.0001331 658.3266 -7.5024312 0.0000000 14
SHAPEIT SUPER AFR - EAS 0 -0.0024804 0.0001650 658.3266 -15.0332256 0.0000000 14
SHAPEIT SUPER AFR - EUR 0 -0.0003192 0.0001438 658.3266 -2.2204313 0.1733737 14
SHAPEIT SUPER AFR - SAS 0 -0.0023074 0.0001554 658.3266 -14.8453584 0.0000000 14
SHAPEIT SUPER AMR - EAS 0 -0.0014819 0.0001749 658.3266 -8.4745259 0.0000000 14
SHAPEIT SUPER AMR - EUR 0 0.0006793 0.0001550 658.3266 4.3829860 0.0001325 14
SHAPEIT SUPER AMR - SAS 0 -0.0013089 0.0001659 658.3266 -7.8910521 0.0000000 14
SHAPEIT SUPER EAS - EUR 0 0.0021612 0.0001831 658.3266 11.8024521 0.0000000 14
SHAPEIT SUPER EAS - SAS 0 0.0001730 0.0001924 658.3266 0.8992391 0.8971656 14
SHAPEIT SUPER EUR - SAS 0 -0.0019882 0.0001745 658.3266 -11.3907276 0.0000000 14
Beagle SUPER AFR - AMR 0 -0.0006261 0.0001426 654.9650 -4.3896754 0.0001287 15
Beagle SUPER AFR - EAS 0 -0.0025961 0.0001768 654.9650 -14.6832093 0.0000000 15
Beagle SUPER AFR - EUR 0 -0.0005065 0.0001541 654.9650 -3.2879788 0.0093636 15
Beagle SUPER AFR - SAS 0 -0.0021253 0.0001666 654.9650 -12.7604077 0.0000000 15
Beagle SUPER AMR - EAS 0 -0.0019700 0.0001874 654.9650 -10.5134461 0.0000000 15
Beagle SUPER AMR - EUR 0 0.0001195 0.0001661 654.9650 0.7197493 0.9519534 15
Beagle SUPER AMR - SAS 0 -0.0014992 0.0001777 654.9650 -8.4350110 0.0000000 15
Beagle SUPER EAS - EUR 0 0.0020896 0.0001962 654.9650 10.6489538 0.0000000 15
Beagle SUPER EAS - SAS 0 0.0004708 0.0002062 654.9650 2.2833077 0.1515599 15
Beagle SUPER EUR - SAS 0 -0.0016188 0.0001870 654.9650 -8.6548396 0.0000000 15
Eagle SUPER AFR - AMR 0 -0.0009513 0.0001426 654.9650 -6.6701033 0.0000000 15
Eagle SUPER AFR - EAS 0 -0.0028416 0.0001768 654.9650 -16.0718895 0.0000000 15
Eagle SUPER AFR - EUR 0 -0.0009448 0.0001541 654.9650 -6.1329436 0.0000000 15
Eagle SUPER AFR - SAS 0 -0.0023409 0.0001666 654.9650 -14.0550598 0.0000000 15
Eagle SUPER AMR - EAS 0 -0.0018903 0.0001874 654.9650 -10.0880715 0.0000000 15
Eagle SUPER AMR - EUR 0 0.0000065 0.0001661 654.9650 0.0391443 0.9999995 15
Eagle SUPER AMR - SAS 0 -0.0013896 0.0001777 654.9650 -7.8183562 0.0000000 15
Eagle SUPER EAS - EUR 0 0.0018968 0.0001962 654.9650 9.6666823 0.0000000 15
Eagle SUPER EAS - SAS 0 0.0005007 0.0002062 654.9650 2.4283110 0.1090845 15
Eagle SUPER EUR - SAS 0 -0.0013961 0.0001870 654.9650 -7.4644868 0.0000000 15
SHAPEIT SUPER AFR - AMR 0 -0.0007169 0.0001426 654.9650 -5.0267370 0.0000064 15
SHAPEIT SUPER AFR - EAS 0 -0.0027182 0.0001768 654.9650 -15.3741071 0.0000000 15
SHAPEIT SUPER AFR - EUR 0 -0.0004102 0.0001541 654.9650 -2.6625197 0.0607778 15
SHAPEIT SUPER AFR - SAS 0 -0.0023991 0.0001666 654.9650 -14.4043760 0.0000000 15
SHAPEIT SUPER AMR - EAS 0 -0.0020013 0.0001874 654.9650 -10.6804703 0.0000000 15
SHAPEIT SUPER AMR - EUR 0 0.0003067 0.0001661 654.9650 1.8469658 0.3474785 15
SHAPEIT SUPER AMR - SAS 0 -0.0016822 0.0001777 654.9650 -9.4643318 0.0000000 15
SHAPEIT SUPER EAS - EUR 0 0.0023081 0.0001962 654.9650 11.7625260 0.0000000 15
SHAPEIT SUPER EAS - SAS 0 0.0003191 0.0002062 654.9650 1.5477744 0.5316887 15
SHAPEIT SUPER EUR - SAS 0 -0.0019889 0.0001870 654.9650 -10.6339192 0.0000000 15
Beagle SUPER AFR - AMR 0 -0.0008256 0.0001565 664.8536 -5.2768148 0.0000018 16
Beagle SUPER AFR - EAS 0 -0.0029272 0.0001940 664.8536 -15.0908585 0.0000000 16
Beagle SUPER AFR - EUR 0 -0.0003634 0.0001690 664.8536 -2.1499089 0.2004070 16
Beagle SUPER AFR - SAS 0 -0.0024435 0.0001827 664.8536 -13.3728041 0.0000000 16
Beagle SUPER AMR - EAS 0 -0.0021016 0.0002056 664.8536 -10.2228684 0.0000000 16
Beagle SUPER AMR - EUR 0 0.0004623 0.0001822 664.8536 2.5371935 0.0837747 16
Beagle SUPER AMR - SAS 0 -0.0016179 0.0001950 664.8536 -8.2970204 0.0000000 16
Beagle SUPER EAS - EUR 0 0.0025639 0.0002153 664.8536 11.9097484 0.0000000 16
Beagle SUPER EAS - SAS 0 0.0004837 0.0002262 664.8536 2.1381830 0.2051714 16
Beagle SUPER EUR - SAS 0 -0.0020802 0.0002052 664.8536 -10.1375261 0.0000000 16
Eagle SUPER AFR - AMR 0 -0.0011030 0.0001565 664.8536 -7.0493982 0.0000000 16
Eagle SUPER AFR - EAS 0 -0.0030829 0.0001940 664.8536 -15.8933189 0.0000000 16
Eagle SUPER AFR - EUR 0 -0.0009101 0.0001690 664.8536 -5.3851443 0.0000010 16
Eagle SUPER AFR - SAS 0 -0.0023353 0.0001827 664.8536 -12.7805433 0.0000000 16
Eagle SUPER AMR - EAS 0 -0.0019799 0.0002056 664.8536 -9.6308900 0.0000000 16
Eagle SUPER AMR - EUR 0 0.0001929 0.0001822 664.8536 1.0584865 0.8276504 16
Eagle SUPER AMR - SAS 0 -0.0012323 0.0001950 664.8536 -6.3197060 0.0000000 16
Eagle SUPER EAS - EUR 0 0.0021727 0.0002153 664.8536 10.0928679 0.0000000 16
Eagle SUPER EAS - SAS 0 0.0007475 0.0002262 664.8536 3.3047323 0.0088475 16
Eagle SUPER EUR - SAS 0 -0.0014252 0.0002052 664.8536 -6.9454656 0.0000000 16
SHAPEIT SUPER AFR - AMR 0 -0.0009145 0.0001565 664.8536 -5.8446828 0.0000001 16
SHAPEIT SUPER AFR - EAS 0 -0.0029446 0.0001940 664.8536 -15.1804752 0.0000000 16
SHAPEIT SUPER AFR - EUR 0 -0.0004172 0.0001690 664.8536 -2.4684448 0.0991237 16
SHAPEIT SUPER AFR - SAS 0 -0.0025304 0.0001827 664.8536 -13.8481551 0.0000000 16
SHAPEIT SUPER AMR - EAS 0 -0.0020301 0.0002056 664.8536 -9.8752113 0.0000000 16
SHAPEIT SUPER AMR - EUR 0 0.0004973 0.0001822 664.8536 2.7293778 0.0508084 16
SHAPEIT SUPER AMR - SAS 0 -0.0016159 0.0001950 664.8536 -8.2867944 0.0000000 16
SHAPEIT SUPER EAS - EUR 0 0.0025274 0.0002153 664.8536 11.7404194 0.0000000 16
SHAPEIT SUPER EAS - SAS 0 0.0004142 0.0002262 664.8536 1.8310444 0.3564806 16
SHAPEIT SUPER EUR - SAS 0 -0.0021132 0.0002052 664.8536 -10.2984605 0.0000000 16
Beagle SUPER AFR - AMR 0 -0.0007964 0.0001560 658.8141 -5.1066707 0.0000043 17
Beagle SUPER AFR - EAS 0 -0.0030315 0.0001933 658.8141 -15.6799025 0.0000000 17
Beagle SUPER AFR - EUR 0 -0.0004975 0.0001685 658.8141 -2.9532303 0.0268961 17
Beagle SUPER AFR - SAS 0 -0.0023810 0.0001821 658.8141 -13.0732794 0.0000000 17
Beagle SUPER AMR - EAS 0 -0.0022351 0.0002049 658.8141 -10.9081681 0.0000000 17
Beagle SUPER AMR - EUR 0 0.0002989 0.0001816 658.8141 1.6459554 0.4685086 17
Beagle SUPER AMR - SAS 0 -0.0015846 0.0001944 658.8141 -8.1528713 0.0000000 17
Beagle SUPER EAS - EUR 0 0.0025340 0.0002146 658.8141 11.8098300 0.0000000 17
Beagle SUPER EAS - SAS 0 0.0006505 0.0002255 658.8141 2.8852531 0.0328256 17
Beagle SUPER EUR - SAS 0 -0.0018835 0.0002045 658.8141 -9.2091583 0.0000000 17
Eagle SUPER AFR - AMR 0 -0.0010447 0.0001560 658.8141 -6.6985295 0.0000000 17
Eagle SUPER AFR - EAS 0 -0.0031568 0.0001933 658.8141 -16.3280326 0.0000000 17
Eagle SUPER AFR - EUR 0 -0.0008668 0.0001685 658.8141 -5.1453290 0.0000035 17
Eagle SUPER AFR - SAS 0 -0.0024999 0.0001821 658.8141 -13.7261569 0.0000000 17
Eagle SUPER AMR - EAS 0 -0.0021121 0.0002049 658.8141 -10.3081226 0.0000000 17
Eagle SUPER AMR - EUR 0 0.0001779 0.0001816 658.8141 0.9796281 0.8644404 17
Eagle SUPER AMR - SAS 0 -0.0014552 0.0001944 658.8141 -7.4873441 0.0000000 17
Eagle SUPER EAS - EUR 0 0.0022900 0.0002146 658.8141 10.6728420 0.0000000 17
Eagle SUPER EAS - SAS 0 0.0006569 0.0002255 658.8141 2.9136444 0.0302238 17
Eagle SUPER EUR - SAS 0 -0.0016331 0.0002045 658.8141 -7.9850405 0.0000000 17
SHAPEIT SUPER AFR - AMR 0 -0.0007836 0.0001560 658.8141 -5.0243014 0.0000065 17
SHAPEIT SUPER AFR - EAS 0 -0.0029472 0.0001933 658.8141 -15.2440201 0.0000000 17
SHAPEIT SUPER AFR - EUR 0 -0.0003464 0.0001685 658.8141 -2.0562725 0.2405994 17
SHAPEIT SUPER AFR - SAS 0 -0.0025388 0.0001821 658.8141 -13.9395701 0.0000000 17
SHAPEIT SUPER AMR - EAS 0 -0.0021637 0.0002049 658.8141 -10.5595790 0.0000000 17
SHAPEIT SUPER AMR - EUR 0 0.0004372 0.0001816 658.8141 2.4072057 0.1146088 17
SHAPEIT SUPER AMR - SAS 0 -0.0017552 0.0001944 658.8141 -9.0307337 0.0000000 17
SHAPEIT SUPER EAS - EUR 0 0.0026008 0.0002146 658.8141 12.1212671 0.0000000 17
SHAPEIT SUPER EAS - SAS 0 0.0004085 0.0002255 658.8141 1.8116907 0.3676003 17
SHAPEIT SUPER EUR - SAS 0 -0.0021924 0.0002045 658.8141 -10.7193448 0.0000000 17
Beagle SUPER AFR - AMR 0 -0.0009327 0.0001291 664.4911 -7.2225102 0.0000000 18
Beagle SUPER AFR - EAS 0 -0.0026788 0.0001601 664.4911 -16.7334623 0.0000000 18
Beagle SUPER AFR - EUR 0 -0.0005296 0.0001395 664.4911 -3.7969750 0.0014986 18
Beagle SUPER AFR - SAS 0 -0.0021673 0.0001508 664.4911 -14.3715377 0.0000000 18
Beagle SUPER AMR - EAS 0 -0.0017462 0.0001697 664.4911 -10.2918582 0.0000000 18
Beagle SUPER AMR - EUR 0 0.0004031 0.0001504 664.4911 2.6802679 0.0579732 18
Beagle SUPER AMR - SAS 0 -0.0012346 0.0001609 664.4911 -7.6716621 0.0000000 18
Beagle SUPER EAS - EUR 0 0.0021492 0.0001777 664.4911 12.0967277 0.0000000 18
Beagle SUPER EAS - SAS 0 0.0005115 0.0001867 664.4911 2.7399718 0.0493654 18
Beagle SUPER EUR - SAS 0 -0.0016377 0.0001694 664.4911 -9.6702971 0.0000000 18
Eagle SUPER AFR - AMR 0 -0.0012486 0.0001291 664.4911 -9.6685518 0.0000000 18
Eagle SUPER AFR - EAS 0 -0.0029528 0.0001601 664.4911 -18.4444619 0.0000000 18
Eagle SUPER AFR - EUR 0 -0.0009995 0.0001395 664.4911 -7.1653340 0.0000000 18
Eagle SUPER AFR - SAS 0 -0.0022907 0.0001508 664.4911 -15.1898541 0.0000000 18
Eagle SUPER AMR - EAS 0 -0.0017042 0.0001697 664.4911 -10.0445600 0.0000000 18
Eagle SUPER AMR - EUR 0 0.0002491 0.0001504 664.4911 1.6564004 0.4618919 18
Eagle SUPER AMR - SAS 0 -0.0010422 0.0001609 664.4911 -6.4757617 0.0000000 18
Eagle SUPER EAS - EUR 0 0.0019533 0.0001777 664.4911 10.9939727 0.0000000 18
Eagle SUPER EAS - SAS 0 0.0006620 0.0001867 664.4911 3.5461514 0.0038204 18
Eagle SUPER EUR - SAS 0 -0.0012913 0.0001694 664.4911 -7.6246878 0.0000000 18
SHAPEIT SUPER AFR - AMR 0 -0.0009898 0.0001291 664.4911 -7.6649213 0.0000000 18
SHAPEIT SUPER AFR - EAS 0 -0.0026590 0.0001601 664.4911 -16.6092307 0.0000000 18
SHAPEIT SUPER AFR - EUR 0 -0.0003802 0.0001395 664.4911 -2.7257526 0.0513110 18
SHAPEIT SUPER AFR - SAS 0 -0.0022900 0.0001508 664.4911 -15.1850913 0.0000000 18
SHAPEIT SUPER AMR - EAS 0 -0.0016691 0.0001697 664.4911 -9.8379098 0.0000000 18
SHAPEIT SUPER AMR - EUR 0 0.0006096 0.0001504 664.4911 4.0538048 0.0005388 18
SHAPEIT SUPER AMR - SAS 0 -0.0013002 0.0001609 664.4911 -8.0790205 0.0000000 18
SHAPEIT SUPER EAS - EUR 0 0.0022788 0.0001777 664.4911 12.8257903 0.0000000 18
SHAPEIT SUPER EAS - SAS 0 0.0003689 0.0001867 664.4911 1.9762561 0.2787537 18
SHAPEIT SUPER EUR - SAS 0 -0.0019098 0.0001694 664.4911 -11.2770529 0.0000000 18
Beagle SUPER AFR - AMR 0 -0.0007560 0.0001427 670.7882 -5.2963722 0.0000016 19
Beagle SUPER AFR - EAS 0 -0.0026431 0.0001770 670.7882 -14.9366944 0.0000000 19
Beagle SUPER AFR - EUR 0 -0.0004454 0.0001542 670.7882 -2.8886689 0.0324874 19
Beagle SUPER AFR - SAS 0 -0.0020292 0.0001667 670.7882 -12.1733821 0.0000000 19
Beagle SUPER AMR - EAS 0 -0.0018871 0.0001875 670.7882 -10.0625194 0.0000000 19
Beagle SUPER AMR - EUR 0 0.0003106 0.0001662 670.7882 1.8687427 0.3353092 19
Beagle SUPER AMR - SAS 0 -0.0012732 0.0001779 670.7882 -7.1573935 0.0000000 19
Beagle SUPER EAS - EUR 0 0.0021978 0.0001964 670.7882 11.1908489 0.0000000 19
Beagle SUPER EAS - SAS 0 0.0006139 0.0002064 670.7882 2.9748722 0.0252022 19
Beagle SUPER EUR - SAS 0 -0.0015839 0.0001872 670.7882 -8.4609891 0.0000000 19
Eagle SUPER AFR - AMR 0 -0.0011415 0.0001427 670.7882 -7.9966881 0.0000000 19
Eagle SUPER AFR - EAS 0 -0.0028256 0.0001770 670.7882 -15.9678166 0.0000000 19
Eagle SUPER AFR - EUR 0 -0.0008699 0.0001542 670.7882 -5.6419124 0.0000002 19
Eagle SUPER AFR - SAS 0 -0.0021593 0.0001667 670.7882 -12.9535031 0.0000000 19
Eagle SUPER AMR - EAS 0 -0.0016841 0.0001875 670.7882 -8.9801814 0.0000000 19
Eagle SUPER AMR - EUR 0 0.0002716 0.0001662 670.7882 1.6337859 0.4762326 19
Eagle SUPER AMR - SAS 0 -0.0010178 0.0001779 670.7882 -5.7216707 0.0000002 19
Eagle SUPER EAS - EUR 0 0.0019557 0.0001964 670.7882 9.9584091 0.0000000 19
Eagle SUPER EAS - SAS 0 0.0006663 0.0002064 670.7882 3.2288992 0.0113691 19
Eagle SUPER EUR - SAS 0 -0.0012894 0.0001872 670.7882 -6.8879997 0.0000000 19
SHAPEIT SUPER AFR - AMR 0 -0.0008285 0.0001427 670.7882 -5.8045254 0.0000001 19
SHAPEIT SUPER AFR - EAS 0 -0.0027275 0.0001770 670.7882 -15.4133644 0.0000000 19
SHAPEIT SUPER AFR - EUR 0 -0.0003478 0.0001542 670.7882 -2.2557195 0.1608399 19
SHAPEIT SUPER AFR - SAS 0 -0.0022152 0.0001667 670.7882 -13.2889796 0.0000000 19
SHAPEIT SUPER AMR - EAS 0 -0.0018989 0.0001875 670.7882 -10.1255213 0.0000000 19
SHAPEIT SUPER AMR - EUR 0 0.0004808 0.0001662 670.7882 2.8922091 0.0321557 19
SHAPEIT SUPER AMR - SAS 0 -0.0013867 0.0001779 670.7882 -7.7950342 0.0000000 19
SHAPEIT SUPER EAS - EUR 0 0.0023797 0.0001964 670.7882 12.1172717 0.0000000 19
SHAPEIT SUPER EAS - SAS 0 0.0005123 0.0002064 670.7882 2.4824504 0.0958170 19
SHAPEIT SUPER EUR - SAS 0 -0.0018674 0.0001872 670.7882 -9.9757321 0.0000000 19
Beagle SUPER AFR - AMR 0 -0.0010025 0.0001552 658.4350 -6.4607980 0.0000000 20
Beagle SUPER AFR - EAS 0 -0.0029490 0.0001924 658.4350 -15.3304764 0.0000000 20
Beagle SUPER AFR - EUR 0 -0.0004579 0.0001676 658.4350 -2.7318575 0.0504773 20
Beagle SUPER AFR - SAS 0 -0.0023596 0.0001812 658.4350 -13.0215001 0.0000000 20
Beagle SUPER AMR - EAS 0 -0.0019465 0.0002039 658.4350 -9.5478089 0.0000000 20
Beagle SUPER AMR - EUR 0 0.0005446 0.0001807 658.4350 3.0141238 0.0224018 20
Beagle SUPER AMR - SAS 0 -0.0013571 0.0001934 658.4350 -7.0177931 0.0000000 20
Beagle SUPER EAS - EUR 0 0.0024911 0.0002135 658.4350 11.6687765 0.0000000 20
Beagle SUPER EAS - SAS 0 0.0005894 0.0002243 658.4350 2.6274413 0.0666120 20
Beagle SUPER EUR - SAS 0 -0.0019017 0.0002035 658.4350 -9.3453807 0.0000000 20
Eagle SUPER AFR - AMR 0 -0.0013225 0.0001552 658.4350 -8.5231533 0.0000000 20
Eagle SUPER AFR - EAS 0 -0.0032978 0.0001924 658.4350 -17.1435811 0.0000000 20
Eagle SUPER AFR - EUR 0 -0.0010072 0.0001676 658.4350 -6.0094283 0.0000000 20
Eagle SUPER AFR - SAS 0 -0.0025136 0.0001812 658.4350 -13.8713466 0.0000000 20
Eagle SUPER AMR - EAS 0 -0.0019752 0.0002039 658.4350 -9.6888847 0.0000000 20
Eagle SUPER AMR - EUR 0 0.0003153 0.0001807 658.4350 1.7449844 0.4070748 20
Eagle SUPER AMR - SAS 0 -0.0011911 0.0001934 658.4350 -6.1593099 0.0000000 20
Eagle SUPER EAS - EUR 0 0.0022906 0.0002135 658.4350 10.7292997 0.0000000 20
Eagle SUPER EAS - SAS 0 0.0007842 0.0002243 658.4350 3.4957079 0.0045785 20
Eagle SUPER EUR - SAS 0 -0.0015064 0.0002035 658.4350 -7.4026250 0.0000000 20
SHAPEIT SUPER AFR - AMR 0 -0.0011291 0.0001552 658.4350 -7.2766280 0.0000000 20
SHAPEIT SUPER AFR - EAS 0 -0.0031237 0.0001924 658.4350 -16.2387427 0.0000000 20
SHAPEIT SUPER AFR - EUR 0 -0.0004334 0.0001676 658.4350 -2.5856776 0.0741610 20
SHAPEIT SUPER AFR - SAS 0 -0.0025271 0.0001812 658.4350 -13.9461593 0.0000000 20
SHAPEIT SUPER AMR - EAS 0 -0.0019946 0.0002039 658.4350 -9.7838695 0.0000000 20
SHAPEIT SUPER AMR - EUR 0 0.0006957 0.0001807 658.4350 3.8502933 0.0012193 20
SHAPEIT SUPER AMR - SAS 0 -0.0013981 0.0001934 658.4350 -7.2296315 0.0000000 20
SHAPEIT SUPER EAS - EUR 0 0.0026903 0.0002135 658.4350 12.6019331 0.0000000 20
SHAPEIT SUPER EAS - SAS 0 0.0005966 0.0002243 658.4350 2.6593599 0.0612799 20
SHAPEIT SUPER EUR - SAS 0 -0.0020938 0.0002035 658.4350 -10.2891744 0.0000000 20
Beagle SUPER AFR - AMR 0 -0.0005208 0.0001435 692.0974 -3.6295654 0.0028108 21
Beagle SUPER AFR - EAS 0 -0.0020027 0.0001779 692.0974 -11.2579978 0.0000000 21
Beagle SUPER AFR - EUR 0 -0.0002092 0.0001550 692.0974 -1.3497751 0.6600462 21
Beagle SUPER AFR - SAS 0 -0.0016937 0.0001676 692.0974 -10.1071134 0.0000000 21
Beagle SUPER AMR - EAS 0 -0.0014819 0.0001885 692.0974 -7.8600821 0.0000000 21
Beagle SUPER AMR - EUR 0 0.0003116 0.0001671 692.0974 1.8648221 0.3374491 21
Beagle SUPER AMR - SAS 0 -0.0011729 0.0001788 692.0974 -6.5586227 0.0000000 21
Beagle SUPER EAS - EUR 0 0.0017935 0.0001974 692.0974 9.0843246 0.0000000 21
Beagle SUPER EAS - SAS 0 0.0003090 0.0002074 692.0974 1.4894484 0.5697001 21
Beagle SUPER EUR - SAS 0 -0.0014845 0.0001882 692.0974 -7.8885002 0.0000000 21
Eagle SUPER AFR - AMR 0 -0.0009006 0.0001435 692.0974 -6.2764647 0.0000000 21
Eagle SUPER AFR - EAS 0 -0.0021879 0.0001779 692.0974 -12.2993288 0.0000000 21
Eagle SUPER AFR - EUR 0 -0.0005696 0.0001550 692.0974 -3.6751158 0.0023733 21
Eagle SUPER AFR - SAS 0 -0.0018760 0.0001676 692.0974 -11.1950386 0.0000000 21
Eagle SUPER AMR - EAS 0 -0.0012873 0.0001885 692.0974 -6.8280330 0.0000000 21
Eagle SUPER AMR - EUR 0 0.0003310 0.0001671 692.0974 1.9809010 0.2763978 21
Eagle SUPER AMR - SAS 0 -0.0009754 0.0001788 692.0974 -5.4541934 0.0000007 21
Eagle SUPER EAS - EUR 0 0.0016183 0.0001974 692.0974 8.1970237 0.0000000 21
Eagle SUPER EAS - SAS 0 0.0003119 0.0002074 692.0974 1.5035868 0.5604695 21
Eagle SUPER EUR - SAS 0 -0.0013064 0.0001882 692.0974 -6.9420424 0.0000000 21
SHAPEIT SUPER AFR - AMR 0 -0.0005376 0.0001435 692.0974 -3.7467632 0.0018110 21
SHAPEIT SUPER AFR - EAS 0 -0.0019671 0.0001779 692.0974 -11.0577831 0.0000000 21
SHAPEIT SUPER AFR - EUR 0 -0.0001291 0.0001550 692.0974 -0.8328976 0.9203687 21
SHAPEIT SUPER AFR - SAS 0 -0.0018169 0.0001676 692.0974 -10.8421074 0.0000000 21
SHAPEIT SUPER AMR - EAS 0 -0.0014294 0.0001885 692.0974 -7.5819655 0.0000000 21
SHAPEIT SUPER AMR - EUR 0 0.0004085 0.0001671 692.0974 2.4448991 0.1048151 21
SHAPEIT SUPER AMR - SAS 0 -0.0012792 0.0001788 692.0974 -7.1533183 0.0000000 21
SHAPEIT SUPER EAS - EUR 0 0.0018380 0.0001974 692.0974 9.3097144 0.0000000 21
SHAPEIT SUPER EAS - SAS 0 0.0001502 0.0002074 692.0974 0.7240361 0.9509401 21
SHAPEIT SUPER EUR - SAS 0 -0.0016878 0.0001882 692.0974 -8.9687205 0.0000000 21
Beagle SUPER AFR - AMR 0 -0.0006224 0.0001654 681.1347 -3.7627727 0.0017057 22
Beagle SUPER AFR - EAS 0 -0.0023871 0.0002051 681.1347 -11.6403070 0.0000000 22
Beagle SUPER AFR - EUR 0 -0.0001454 0.0001787 681.1347 -0.8136906 0.9264331 22
Beagle SUPER AFR - SAS 0 -0.0020017 0.0001932 681.1347 -10.3618521 0.0000000 22
Beagle SUPER AMR - EAS 0 -0.0017647 0.0002173 681.1347 -8.1194277 0.0000000 22
Beagle SUPER AMR - EUR 0 0.0004771 0.0001926 681.1347 2.4764627 0.0971961 22
Beagle SUPER AMR - SAS 0 -0.0013793 0.0002062 681.1347 -6.6904427 0.0000000 22
Beagle SUPER EAS - EUR 0 0.0022417 0.0002276 681.1347 9.8496764 0.0000000 22
Beagle SUPER EAS - SAS 0 0.0003854 0.0002391 681.1347 1.6115084 0.4904665 22
Beagle SUPER EUR - SAS 0 -0.0018563 0.0002169 681.1347 -8.5568803 0.0000000 22
Eagle SUPER AFR - AMR 0 -0.0009613 0.0001654 681.1347 -5.8108932 0.0000001 22
Eagle SUPER AFR - EAS 0 -0.0026950 0.0002051 681.1347 -13.1415978 0.0000000 22
Eagle SUPER AFR - EUR 0 -0.0006037 0.0001787 681.1347 -3.3784911 0.0068813 22
Eagle SUPER AFR - SAS 0 -0.0022285 0.0001932 681.1347 -11.5356567 0.0000000 22
Eagle SUPER AMR - EAS 0 -0.0017338 0.0002173 681.1347 -7.9771222 0.0000000 22
Eagle SUPER AMR - EUR 0 0.0003576 0.0001926 681.1347 1.8562377 0.3422421 22
Eagle SUPER AMR - SAS 0 -0.0012672 0.0002062 681.1347 -6.1469507 0.0000000 22
Eagle SUPER EAS - EUR 0 0.0020913 0.0002276 681.1347 9.1888256 0.0000000 22
Eagle SUPER EAS - SAS 0 0.0004665 0.0002391 681.1347 1.9506974 0.2916399 22
Eagle SUPER EUR - SAS 0 -0.0016248 0.0002169 681.1347 -7.4896687 0.0000000 22
SHAPEIT SUPER AFR - AMR 0 -0.0006362 0.0001654 681.1347 -3.8456205 0.0012382 22
SHAPEIT SUPER AFR - EAS 0 -0.0024011 0.0002051 681.1347 -11.7085075 0.0000000 22
SHAPEIT SUPER AFR - EUR 0 -0.0000307 0.0001787 681.1347 -0.1717224 0.9998051 22
SHAPEIT SUPER AFR - SAS 0 -0.0022147 0.0001932 681.1347 -11.4640855 0.0000000 22
SHAPEIT SUPER AMR - EAS 0 -0.0017650 0.0002173 681.1347 -8.1207219 0.0000000 22
SHAPEIT SUPER AMR - EUR 0 0.0006055 0.0001926 681.1347 3.1430717 0.0149867 22
SHAPEIT SUPER AMR - SAS 0 -0.0015785 0.0002062 681.1347 -7.6568274 0.0000000 22
SHAPEIT SUPER EAS - EUR 0 0.0023704 0.0002276 681.1347 10.4151285 0.0000000 22
SHAPEIT SUPER EAS - SAS 0 0.0001864 0.0002391 681.1347 0.7796125 0.9364814 22
SHAPEIT SUPER EUR - SAS 0 -0.0021840 0.0002169 681.1347 -10.0671510 0.0000000 22
Beagle SUPER AFR - AMR 0 -0.0000929 0.0000362 1191.1198 -2.5662199 0.0773715 23
Beagle SUPER AFR - EAS 0 -0.0009474 0.0000362 1191.1198 -26.1746698 0.0000000 23
Beagle SUPER AFR - EUR 0 -0.0002343 0.0000362 1191.1198 -6.4729229 0.0000000 23
Beagle SUPER AFR - SAS 0 -0.0005822 0.0000362 1191.1198 -16.0858537 0.0000000 23
Beagle SUPER AMR - EAS 0 -0.0008545 0.0000362 1191.1198 -23.6084499 0.0000000 23
Beagle SUPER AMR - EUR 0 -0.0001414 0.0000362 1191.1198 -3.9067030 0.0009367 23
Beagle SUPER AMR - SAS 0 -0.0004893 0.0000362 1191.1198 -13.5196338 0.0000000 23
Beagle SUPER EAS - EUR 0 0.0007131 0.0000362 1191.1198 19.7017469 0.0000000 23
Beagle SUPER EAS - SAS 0 0.0003652 0.0000362 1191.1198 10.0888161 0.0000000 23
Beagle SUPER EUR - SAS 0 -0.0003479 0.0000362 1191.1198 -9.6129308 0.0000000 23
Eagle SUPER AFR - AMR 0 -0.0000811 0.0000362 1191.1198 -2.2406667 0.1655198 23
Eagle SUPER AFR - EAS 0 -0.0009436 0.0000362 1191.1198 -26.0697877 0.0000000 23
Eagle SUPER AFR - EUR 0 -0.0002314 0.0000362 1191.1198 -6.3923197 0.0000000 23
Eagle SUPER AFR - SAS 0 -0.0006230 0.0000362 1191.1198 -17.2117010 0.0000000 23
Eagle SUPER AMR - EAS 0 -0.0008625 0.0000362 1191.1198 -23.8291210 0.0000000 23
Eagle SUPER AMR - EUR 0 -0.0001503 0.0000362 1191.1198 -4.1516530 0.0003406 23
Eagle SUPER AMR - SAS 0 -0.0005419 0.0000362 1191.1198 -14.9710343 0.0000000 23
Eagle SUPER EAS - EUR 0 0.0007122 0.0000362 1191.1198 19.6774680 0.0000000 23
Eagle SUPER EAS - SAS 0 0.0003206 0.0000362 1191.1198 8.8580867 0.0000000 23
Eagle SUPER EUR - SAS 0 -0.0003916 0.0000362 1191.1198 -10.8193813 0.0000000 23
SHAPEIT SUPER AFR - AMR 0 -0.0000758 0.0000362 1191.1198 -2.0954508 0.2226251 23
SHAPEIT SUPER AFR - EAS 0 -0.0009169 0.0000362 1191.1198 -25.3317416 0.0000000 23
SHAPEIT SUPER AFR - EUR 0 -0.0002284 0.0000362 1191.1198 -6.3112132 0.0000000 23
SHAPEIT SUPER AFR - SAS 0 -0.0006043 0.0000362 1191.1198 -16.6950759 0.0000000 23
SHAPEIT SUPER AMR - EAS 0 -0.0008410 0.0000362 1191.1198 -23.2362908 0.0000000 23
SHAPEIT SUPER AMR - EUR 0 -0.0001526 0.0000362 1191.1198 -4.2157624 0.0002588 23
SHAPEIT SUPER AMR - SAS 0 -0.0005284 0.0000362 1191.1198 -14.5996251 0.0000000 23
SHAPEIT SUPER EAS - EUR 0 0.0006885 0.0000362 1191.1198 19.0205284 0.0000000 23
SHAPEIT SUPER EAS - SAS 0 0.0003126 0.0000362 1191.1198 8.6366657 0.0000000 23
SHAPEIT SUPER EUR - SAS 0 -0.0003758 0.0000362 1191.1198 -10.3838627 0.0000000 23

Total Errors

cross_meth_plot <- function(df, p_title, p_func, pop, chrom=as.character(chrom)) {
  p1 <- p_func(df, "Beagle", "SHAPEIT", pop, chrom = chrom)
  p_legend <- cowplot::get_legend(p1)
  
  p1 <- p1 + guides(colour="none") + ggtitle(p_title, paste0("Chromosome ", chrom))
  
  p2 <- p_func(df, "Beagle", "Eagle", pop, chrom = chrom) +
    guides(colour="none") + ggtitle("", "")
  
  p3 <- p_func(df, "SHAPEIT", "Eagle", pop, chrom = chrom) +
    guides(colour="none") + ggtitle("", "")
  
  return(grid.arrange(p1, p_legend, p2, p3, ncol = 2))
  }

plot_total_errors <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_other_beagle + n_flip_beagle),
         Eagle =  (n_other_eagle + n_flip_eagle),
         SHAPEIT =  (n_other_shapeit + n_flip_shapeit)) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Errors", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_total_errors_noth <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_switch_b + n_flip_b),
         Eagle =  (n_switch_e + n_flip_e),
         SHAPEIT =  (n_switch_s + n_flip_s)) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Errors", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

table_total_errors <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_other_beagle + n_flip_beagle),
         Eagle =  (n_other_eagle + n_flip_eagle),
         SHAPEIT =  (n_other_shapeit + n_flip_shapeit)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_e_e = factor(Beagle == Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_e_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

table_total_errors_noth <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_switch_b + n_flip_b),
         Eagle =  (n_switch_e + n_flip_e),
         SHAPEIT =  (n_switch_s + n_flip_s)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_e_e = factor(Beagle == Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_e_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

Chromosome 1

chrom <- 1

df_switch_trio_noth <- df_switch_trio_noth %>%
  left_join({df_subj_rel %>% select(SUPER, id2)}, by = c("sample" = "id2"))

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
cb6aa66 Andy Beck 2024-06-06
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 187 (93%) 51 (37%) 14 (19%) 34 (32%) 38 (45%)
    TRUE 14 (7.0%) 86 (63%) 58 (81%) 73 (68%) 47 (55%)
b_e_e




    FALSE 200 (100%) 136 (99%) 71 (99%) 105 (98%) 84 (99%)
    TRUE 1 (0.5%) 1 (0.7%) 1 (1.4%) 2 (1.9%) 1 (1.2%)
b_l_s




    FALSE 11 (5.5%) 3 (2.2%) 5 (6.9%) 8 (7.5%) 0 (0%)
    TRUE 190 (95%) 134 (98%) 67 (93%) 99 (93%) 85 (100%)
e_l_b




    FALSE 15 (7.5%) 87 (64%) 59 (82%) 75 (70%) 48 (56%)
    TRUE 186 (93%) 50 (36%) 13 (18%) 32 (30%) 37 (44%)
e_l_s




    FALSE 4 (2.0%) 31 (23%) 34 (47%) 31 (29%) 3 (3.5%)
    TRUE 197 (98%) 106 (77%) 38 (53%) 76 (71%) 82 (96%)
s_l_b




    FALSE 191 (95%) 134 (98%) 67 (93%) 100 (93%) 85 (100%)
    TRUE 10 (5.0%) 3 (2.2%) 5 (6.9%) 7 (6.5%) 0 (0%)
s_l_e




    FALSE 197 (98%) 108 (79%) 38 (53%) 77 (72%) 82 (96%)
    TRUE 4 (2.0%) 29 (21%) 34 (47%) 30 (28%) 3 (3.5%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 196 (98%) 73 (53%) 25 (35%) 43 (40%) 46 (54%)
    TRUE 5 (2.5%) 64 (47%) 47 (65%) 64 (60%) 39 (46%)
b_e_e




    FALSE 201 (100%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
b_l_s




    FALSE 9 (4.5%) 8 (5.8%) 6 (8.3%) 19 (18%) 1 (1.2%)
    TRUE 192 (96%) 129 (94%) 66 (92%) 88 (82%) 84 (99%)
e_l_b




    FALSE 5 (2.5%) 64 (47%) 47 (65%) 65 (61%) 39 (46%)
    TRUE 196 (98%) 73 (53%) 25 (35%) 42 (39%) 46 (54%)
e_l_s




    FALSE 1 (0.5%) 20 (15%) 19 (26%) 23 (21%) 2 (2.4%)
    TRUE 200 (100%) 117 (85%) 53 (74%) 84 (79%) 83 (98%)
s_l_b




    FALSE 192 (96%) 130 (95%) 66 (92%) 88 (82%) 84 (99%)
    TRUE 9 (4.5%) 7 (5.1%) 6 (8.3%) 19 (18%) 1 (1.2%)
s_l_e




    FALSE 200 (100%) 118 (86%) 54 (75%) 85 (79%) 83 (98%)
    TRUE 1 (0.5%) 19 (14%) 18 (25%) 22 (21%) 2 (2.4%)
1 n (%)

Chromosome 2

chrom <- 2
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 184 (92%) 63 (46%) 15 (21%) 40 (37%) 42 (49%)
    TRUE 17 (8.5%) 74 (54%) 57 (79%) 67 (63%) 43 (51%)
b_e_e




    FALSE 201 (100%) 135 (99%) 72 (100%) 105 (98%) 84 (99%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 2 (1.9%) 1 (1.2%)
b_l_s




    FALSE 11 (5.5%) 8 (5.8%) 6 (8.3%) 12 (11%) 2 (2.4%)
    TRUE 190 (95%) 129 (94%) 66 (92%) 95 (89%) 83 (98%)
e_l_b




    FALSE 17 (8.5%) 76 (55%) 57 (79%) 69 (64%) 44 (52%)
    TRUE 184 (92%) 61 (45%) 15 (21%) 38 (36%) 41 (48%)
e_l_s




    FALSE 1 (0.5%) 26 (19%) 19 (26%) 27 (25%) 4 (4.7%)
    TRUE 200 (100%) 111 (81%) 53 (74%) 80 (75%) 81 (95%)
s_l_b




    FALSE 190 (95%) 130 (95%) 66 (92%) 97 (91%) 83 (98%)
    TRUE 11 (5.5%) 7 (5.1%) 6 (8.3%) 10 (9.3%) 2 (2.4%)
s_l_e




    FALSE 200 (100%) 112 (82%) 53 (74%) 82 (77%) 81 (95%)
    TRUE 1 (0.5%) 25 (18%) 19 (26%) 25 (23%) 4 (4.7%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 186 (93%) 81 (59%) 22 (31%) 60 (56%) 55 (65%)
    TRUE 15 (7.5%) 56 (41%) 50 (69%) 47 (44%) 30 (35%)
b_e_e




    FALSE 201 (100%) 135 (99%) 70 (97%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 2 (1.5%) 2 (2.8%) 1 (0.9%) 0 (0%)
b_l_s




    FALSE 10 (5.0%) 6 (4.4%) 1 (1.4%) 6 (5.6%) 1 (1.2%)
    TRUE 191 (95%) 131 (96%) 71 (99%) 101 (94%) 84 (99%)
e_l_b




    FALSE 15 (7.5%) 58 (42%) 52 (72%) 48 (45%) 30 (35%)
    TRUE 186 (93%) 79 (58%) 20 (28%) 59 (55%) 55 (65%)
e_l_s




    FALSE 2 (1.0%) 24 (18%) 9 (13%) 11 (10%) 0 (0%)
    TRUE 199 (99%) 113 (82%) 63 (88%) 96 (90%) 85 (100%)
s_l_b




    FALSE 192 (96%) 131 (96%) 71 (99%) 101 (94%) 84 (99%)
    TRUE 9 (4.5%) 6 (4.4%) 1 (1.4%) 6 (5.6%) 1 (1.2%)
s_l_e




    FALSE 199 (99%) 113 (82%) 63 (88%) 96 (90%) 85 (100%)
    TRUE 2 (1.0%) 24 (18%) 9 (13%) 11 (10%) 0 (0%)
1 n (%)

Chromosome 3

chrom <- 3
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 187 (93%) 56 (41%) 16 (22%) 34 (32%) 39 (46%)
    TRUE 14 (7.0%) 81 (59%) 56 (78%) 73 (68%) 46 (54%)
b_e_e




    FALSE 201 (100%) 135 (99%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 1 (0.9%) 0 (0%)
b_l_s




    FALSE 14 (7.0%) 7 (5.1%) 6 (8.3%) 12 (11%) 3 (3.5%)
    TRUE 187 (93%) 130 (95%) 66 (92%) 95 (89%) 82 (96%)
e_l_b




    FALSE 14 (7.0%) 83 (61%) 56 (78%) 74 (69%) 46 (54%)
    TRUE 187 (93%) 54 (39%) 16 (22%) 33 (31%) 39 (46%)
e_l_s




    FALSE 1 (0.5%) 30 (22%) 25 (35%) 29 (27%) 9 (11%)
    TRUE 200 (100%) 107 (78%) 47 (65%) 78 (73%) 76 (89%)
s_l_b




    FALSE 188 (94%) 130 (95%) 66 (92%) 98 (92%) 82 (96%)
    TRUE 13 (6.5%) 7 (5.1%) 6 (8.3%) 9 (8.4%) 3 (3.5%)
s_l_e




    FALSE 200 (100%) 108 (79%) 48 (67%) 78 (73%) 76 (89%)
    TRUE 1 (0.5%) 29 (21%) 24 (33%) 29 (27%) 9 (11%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 192 (96%) 78 (57%) 24 (33%) 57 (53%) 55 (65%)
    TRUE 9 (4.5%) 59 (43%) 48 (67%) 50 (47%) 30 (35%)
b_e_e




    FALSE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 1 (1.2%)
b_l_s




    FALSE 7 (3.5%) 8 (5.8%) 4 (5.6%) 12 (11%) 0 (0%)
    TRUE 194 (97%) 129 (94%) 68 (94%) 95 (89%) 85 (100%)
e_l_b




    FALSE 9 (4.5%) 61 (45%) 48 (67%) 50 (47%) 31 (36%)
    TRUE 192 (96%) 76 (55%) 24 (33%) 57 (53%) 54 (64%)
e_l_s




    FALSE 1 (0.5%) 17 (12%) 20 (28%) 14 (13%) 2 (2.4%)
    TRUE 200 (100%) 120 (88%) 52 (72%) 93 (87%) 83 (98%)
s_l_b




    FALSE 194 (97%) 130 (95%) 68 (94%) 98 (92%) 85 (100%)
    TRUE 7 (3.5%) 7 (5.1%) 4 (5.6%) 9 (8.4%) 0 (0%)
s_l_e




    FALSE 200 (100%) 121 (88%) 54 (75%) 93 (87%) 83 (98%)
    TRUE 1 (0.5%) 16 (12%) 18 (25%) 14 (13%) 2 (2.4%)
1 n (%)

Chromosome 4

chrom <- 4
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 178 (89%) 56 (41%) 12 (17%) 29 (27%) 37 (44%)
    TRUE 23 (11%) 81 (59%) 60 (83%) 78 (73%) 48 (56%)
b_e_e




    FALSE 200 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
b_l_s




    FALSE 16 (8.0%) 6 (4.4%) 1 (1.4%) 14 (13%) 3 (3.5%)
    TRUE 185 (92%) 131 (96%) 71 (99%) 93 (87%) 82 (96%)
e_l_b




    FALSE 24 (12%) 82 (60%) 60 (83%) 78 (73%) 48 (56%)
    TRUE 177 (88%) 55 (40%) 12 (17%) 29 (27%) 37 (44%)
e_l_s




    FALSE 9 (4.5%) 28 (20%) 35 (49%) 30 (28%) 4 (4.7%)
    TRUE 192 (96%) 109 (80%) 37 (51%) 77 (72%) 81 (95%)
s_l_b




    FALSE 186 (93%) 131 (96%) 71 (99%) 93 (87%) 82 (96%)
    TRUE 15 (7.5%) 6 (4.4%) 1 (1.4%) 14 (13%) 3 (3.5%)
s_l_e




    FALSE 192 (96%) 110 (80%) 37 (51%) 77 (72%) 81 (95%)
    TRUE 9 (4.5%) 27 (20%) 35 (49%) 30 (28%) 4 (4.7%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 188 (94%) 68 (50%) 13 (18%) 47 (44%) 55 (65%)
    TRUE 13 (6.5%) 69 (50%) 59 (82%) 60 (56%) 30 (35%)
b_e_e




    FALSE 200 (100%) 136 (99%) 72 (100%) 105 (98%) 82 (96%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 2 (1.9%) 3 (3.5%)
b_l_s




    FALSE 21 (10%) 12 (8.8%) 2 (2.8%) 9 (8.4%) 3 (3.5%)
    TRUE 180 (90%) 125 (91%) 70 (97%) 98 (92%) 82 (96%)
e_l_b




    FALSE 14 (7.0%) 70 (51%) 59 (82%) 62 (58%) 33 (39%)
    TRUE 187 (93%) 67 (49%) 13 (18%) 45 (42%) 52 (61%)
e_l_s




    FALSE 3 (1.5%) 24 (18%) 20 (28%) 13 (12%) 5 (5.9%)
    TRUE 198 (99%) 113 (82%) 52 (72%) 94 (88%) 80 (94%)
s_l_b




    FALSE 180 (90%) 125 (91%) 70 (97%) 98 (92%) 82 (96%)
    TRUE 21 (10%) 12 (8.8%) 2 (2.8%) 9 (8.4%) 3 (3.5%)
s_l_e




    FALSE 198 (99%) 114 (83%) 53 (74%) 94 (88%) 80 (94%)
    TRUE 3 (1.5%) 23 (17%) 19 (26%) 13 (12%) 5 (5.9%)
1 n (%)

Chromosome 5

chrom <- 5
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 186 (93%) 61 (45%) 14 (19%) 46 (43%) 47 (55%)
    TRUE 15 (7.5%) 76 (55%) 58 (81%) 61 (57%) 38 (45%)
b_e_e




    FALSE 200 (100%) 137 (100%) 71 (99%) 106 (99%) 82 (96%)
    TRUE 1 (0.5%) 0 (0%) 1 (1.4%) 1 (0.9%) 3 (3.5%)
b_l_s




    FALSE 7 (3.5%) 8 (5.8%) 5 (6.9%) 12 (11%) 2 (2.4%)
    TRUE 194 (97%) 129 (94%) 67 (93%) 95 (89%) 83 (98%)
e_l_b




    FALSE 16 (8.0%) 76 (55%) 59 (82%) 62 (58%) 41 (48%)
    TRUE 185 (92%) 61 (45%) 13 (18%) 45 (42%) 44 (52%)
e_l_s




    FALSE 1 (0.5%) 20 (15%) 27 (38%) 27 (25%) 5 (5.9%)
    TRUE 200 (100%) 117 (85%) 45 (63%) 80 (75%) 80 (94%)
s_l_b




    FALSE 194 (97%) 130 (95%) 67 (93%) 96 (90%) 83 (98%)
    TRUE 7 (3.5%) 7 (5.1%) 5 (6.9%) 11 (10%) 2 (2.4%)
s_l_e




    FALSE 200 (100%) 117 (85%) 47 (65%) 81 (76%) 80 (94%)
    TRUE 1 (0.5%) 20 (15%) 25 (35%) 26 (24%) 5 (5.9%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 189 (94%) 76 (55%) 23 (32%) 57 (53%) 53 (62%)
    TRUE 12 (6.0%) 61 (45%) 49 (68%) 50 (47%) 32 (38%)
b_e_e




    FALSE 201 (100%) 134 (98%) 72 (100%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 17 (8.5%) 7 (5.1%) 2 (2.8%) 12 (11%) 2 (2.4%)
    TRUE 184 (92%) 130 (95%) 70 (97%) 95 (89%) 83 (98%)
e_l_b




    FALSE 12 (6.0%) 64 (47%) 49 (68%) 52 (49%) 32 (38%)
    TRUE 189 (94%) 73 (53%) 23 (32%) 55 (51%) 53 (62%)
e_l_s




    FALSE 4 (2.0%) 20 (15%) 12 (17%) 22 (21%) 1 (1.2%)
    TRUE 197 (98%) 117 (85%) 60 (83%) 85 (79%) 84 (99%)
s_l_b




    FALSE 185 (92%) 130 (95%) 70 (97%) 95 (89%) 84 (99%)
    TRUE 16 (8.0%) 7 (5.1%) 2 (2.8%) 12 (11%) 1 (1.2%)
s_l_e




    FALSE 197 (98%) 118 (86%) 60 (83%) 86 (80%) 84 (99%)
    TRUE 4 (2.0%) 19 (14%) 12 (17%) 21 (20%) 1 (1.2%)
1 n (%)

Chromosome 6

chrom <- 6
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 169 (84%) 55 (40%) 12 (17%) 41 (38%) 39 (46%)
    TRUE 32 (16%) 82 (60%) 60 (83%) 66 (62%) 46 (54%)
b_e_e




    FALSE 200 (100%) 134 (98%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 1 (0.5%) 3 (2.2%) 0 (0%) 0 (0%) 0 (0%)
b_l_s




    FALSE 6 (3.0%) 13 (9.5%) 3 (4.2%) 12 (11%) 3 (3.5%)
    TRUE 195 (97%) 124 (91%) 69 (96%) 95 (89%) 82 (96%)
e_l_b




    FALSE 33 (16%) 85 (62%) 60 (83%) 66 (62%) 46 (54%)
    TRUE 168 (84%) 52 (38%) 12 (17%) 41 (38%) 39 (46%)
e_l_s




    FALSE 6 (3.0%) 34 (25%) 32 (44%) 27 (25%) 7 (8.2%)
    TRUE 195 (97%) 103 (75%) 40 (56%) 80 (75%) 78 (92%)
s_l_b




    FALSE 195 (97%) 124 (91%) 69 (96%) 96 (90%) 83 (98%)
    TRUE 6 (3.0%) 13 (9.5%) 3 (4.2%) 11 (10%) 2 (2.4%)
s_l_e




    FALSE 195 (97%) 104 (76%) 42 (58%) 83 (78%) 78 (92%)
    TRUE 6 (3.0%) 33 (24%) 30 (42%) 24 (22%) 7 (8.2%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 185 (92%) 74 (54%) 18 (25%) 53 (50%) 49 (58%)
    TRUE 16 (8.0%) 63 (46%) 54 (75%) 54 (50%) 36 (42%)
b_e_e




    FALSE 201 (100%) 134 (98%) 71 (99%) 105 (98%) 84 (99%)
    TRUE 0 (0%) 3 (2.2%) 1 (1.4%) 2 (1.9%) 1 (1.2%)
b_l_s




    FALSE 12 (6.0%) 9 (6.6%) 5 (6.9%) 13 (12%) 4 (4.7%)
    TRUE 189 (94%) 128 (93%) 67 (93%) 94 (88%) 81 (95%)
e_l_b




    FALSE 16 (8.0%) 66 (48%) 55 (76%) 56 (52%) 37 (44%)
    TRUE 185 (92%) 71 (52%) 17 (24%) 51 (48%) 48 (56%)
e_l_s




    FALSE 3 (1.5%) 28 (20%) 22 (31%) 20 (19%) 3 (3.5%)
    TRUE 198 (99%) 109 (80%) 50 (69%) 87 (81%) 82 (96%)
s_l_b




    FALSE 190 (95%) 128 (93%) 67 (93%) 95 (89%) 82 (96%)
    TRUE 11 (5.5%) 9 (6.6%) 5 (6.9%) 12 (11%) 3 (3.5%)
s_l_e




    FALSE 198 (99%) 110 (80%) 52 (72%) 90 (84%) 83 (98%)
    TRUE 3 (1.5%) 27 (20%) 20 (28%) 17 (16%) 2 (2.4%)
1 n (%)

Chromosome 7

chrom <- 7
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 172 (86%) 51 (37%) 13 (18%) 33 (31%) 35 (41%)
    TRUE 29 (14%) 86 (63%) 59 (82%) 74 (69%) 50 (59%)
b_e_e




    FALSE 198 (99%) 137 (100%) 72 (100%) 104 (97%) 85 (100%)
    TRUE 3 (1.5%) 0 (0%) 0 (0%) 3 (2.8%) 0 (0%)
b_l_s




    FALSE 27 (13%) 2 (1.5%) 4 (5.6%) 20 (19%) 2 (2.4%)
    TRUE 174 (87%) 135 (99%) 68 (94%) 87 (81%) 83 (98%)
e_l_b




    FALSE 32 (16%) 86 (63%) 59 (82%) 77 (72%) 50 (59%)
    TRUE 169 (84%) 51 (37%) 13 (18%) 30 (28%) 35 (41%)
e_l_s




    FALSE 5 (2.5%) 30 (22%) 31 (43%) 43 (40%) 11 (13%)
    TRUE 196 (98%) 107 (78%) 41 (57%) 64 (60%) 74 (87%)
s_l_b




    FALSE 176 (88%) 135 (99%) 68 (94%) 87 (81%) 83 (98%)
    TRUE 25 (12%) 2 (1.5%) 4 (5.6%) 20 (19%) 2 (2.4%)
s_l_e




    FALSE 196 (98%) 108 (79%) 43 (60%) 64 (60%) 74 (87%)
    TRUE 5 (2.5%) 29 (21%) 29 (40%) 43 (40%) 11 (13%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 177 (88%) 75 (55%) 28 (39%) 44 (41%) 53 (62%)
    TRUE 24 (12%) 62 (45%) 44 (61%) 63 (59%) 32 (38%)
b_e_e




    FALSE 199 (99%) 135 (99%) 72 (100%) 107 (100%) 83 (98%)
    TRUE 2 (1.0%) 2 (1.5%) 0 (0%) 0 (0%) 2 (2.4%)
b_l_s




    FALSE 23 (11%) 11 (8.0%) 6 (8.3%) 19 (18%) 2 (2.4%)
    TRUE 178 (89%) 126 (92%) 66 (92%) 88 (82%) 83 (98%)
e_l_b




    FALSE 26 (13%) 64 (47%) 44 (61%) 63 (59%) 34 (40%)
    TRUE 175 (87%) 73 (53%) 28 (39%) 44 (41%) 51 (60%)
e_l_s




    FALSE 2 (1.0%) 26 (19%) 17 (24%) 26 (24%) 3 (3.5%)
    TRUE 199 (99%) 111 (81%) 55 (76%) 81 (76%) 82 (96%)
s_l_b




    FALSE 178 (89%) 126 (92%) 66 (92%) 89 (83%) 83 (98%)
    TRUE 23 (11%) 11 (8.0%) 6 (8.3%) 18 (17%) 2 (2.4%)
s_l_e




    FALSE 199 (99%) 112 (82%) 55 (76%) 82 (77%) 82 (96%)
    TRUE 2 (1.0%) 25 (18%) 17 (24%) 25 (23%) 3 (3.5%)
1 n (%)

Chromosome 8

chrom <- 8
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
17d41d5 Andy Beck 2024-05-22
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 47 (23%) 9 (6.6%) 1 (1.4%) 2 (1.9%) 5 (5.9%)
    TRUE 154 (77%) 128 (93%) 71 (99%) 105 (98%) 80 (94%)
b_e_e




    FALSE 200 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
b_l_s




    FALSE 133 (66%) 79 (58%) 60 (83%) 67 (63%) 50 (59%)
    TRUE 68 (34%) 58 (42%) 12 (17%) 40 (37%) 35 (41%)
e_l_b




    FALSE 155 (77%) 129 (94%) 71 (99%) 105 (98%) 80 (94%)
    TRUE 46 (23%) 8 (5.8%) 1 (1.4%) 2 (1.9%) 5 (5.9%)
e_l_s




    FALSE 144 (72%) 110 (80%) 71 (99%) 88 (82%) 56 (66%)
    TRUE 57 (28%) 27 (20%) 1 (1.4%) 19 (18%) 29 (34%)
s_l_b




    FALSE 71 (35%) 62 (45%) 14 (19%) 43 (40%) 36 (42%)
    TRUE 130 (65%) 75 (55%) 58 (81%) 64 (60%) 49 (58%)
s_l_e




    FALSE 58 (29%) 27 (20%) 1 (1.4%) 19 (18%) 29 (34%)
    TRUE 143 (71%) 110 (80%) 71 (99%) 88 (82%) 56 (66%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 187 (93%) 68 (50%) 28 (39%) 58 (54%) 53 (62%)
    TRUE 14 (7.0%) 69 (50%) 44 (61%) 49 (46%) 32 (38%)
b_e_e




    FALSE 201 (100%) 135 (99%) 70 (97%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 2 (1.5%) 2 (2.8%) 0 (0%) 1 (1.2%)
b_l_s




    FALSE 16 (8.0%) 11 (8.0%) 16 (22%) 15 (14%) 6 (7.1%)
    TRUE 185 (92%) 126 (92%) 56 (78%) 92 (86%) 79 (93%)
e_l_b




    FALSE 14 (7.0%) 71 (52%) 46 (64%) 49 (46%) 33 (39%)
    TRUE 187 (93%) 66 (48%) 26 (36%) 58 (54%) 52 (61%)
e_l_s




    FALSE 1 (0.5%) 20 (15%) 23 (32%) 25 (23%) 4 (4.7%)
    TRUE 200 (100%) 117 (85%) 49 (68%) 82 (77%) 81 (95%)
s_l_b




    FALSE 187 (93%) 126 (92%) 56 (78%) 92 (86%) 80 (94%)
    TRUE 14 (7.0%) 11 (8.0%) 16 (22%) 15 (14%) 5 (5.9%)
s_l_e




    FALSE 200 (100%) 118 (86%) 51 (71%) 82 (77%) 81 (95%)
    TRUE 1 (0.5%) 19 (14%) 21 (29%) 25 (23%) 4 (4.7%)
1 n (%)

Chromosome 9

chrom <- 9
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 166 (83%) 58 (42%) 13 (18%) 39 (36%) 48 (56%)
    TRUE 35 (17%) 79 (58%) 59 (82%) 68 (64%) 37 (44%)
b_e_e




    FALSE 200 (100%) 137 (100%) 72 (100%) 104 (97%) 85 (100%)
    TRUE 1 (0.5%) 0 (0%) 0 (0%) 3 (2.8%) 0 (0%)
b_l_s




    FALSE 33 (16%) 16 (12%) 9 (13%) 23 (21%) 8 (9.4%)
    TRUE 168 (84%) 121 (88%) 63 (88%) 84 (79%) 77 (91%)
e_l_b




    FALSE 36 (18%) 79 (58%) 59 (82%) 71 (66%) 37 (44%)
    TRUE 165 (82%) 58 (42%) 13 (18%) 36 (34%) 48 (56%)
e_l_s




    FALSE 14 (7.0%) 30 (22%) 32 (44%) 43 (40%) 9 (11%)
    TRUE 187 (93%) 107 (78%) 40 (56%) 64 (60%) 76 (89%)
s_l_b




    FALSE 170 (85%) 121 (88%) 63 (88%) 85 (79%) 78 (92%)
    TRUE 31 (15%) 16 (12%) 9 (13%) 22 (21%) 7 (8.2%)
s_l_e




    FALSE 188 (94%) 107 (78%) 41 (57%) 67 (63%) 77 (91%)
    TRUE 13 (6.5%) 30 (22%) 31 (43%) 40 (37%) 8 (9.4%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 181 (90%) 73 (53%) 18 (25%) 51 (48%) 53 (62%)
    TRUE 20 (10.0%) 64 (47%) 54 (75%) 56 (52%) 32 (38%)
b_e_e




    FALSE 200 (100%) 136 (99%) 72 (100%) 105 (98%) 85 (100%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 29 (14%) 10 (7.3%) 8 (11%) 18 (17%) 8 (9.4%)
    TRUE 172 (86%) 127 (93%) 64 (89%) 89 (83%) 77 (91%)
e_l_b




    FALSE 21 (10%) 65 (47%) 54 (75%) 58 (54%) 32 (38%)
    TRUE 180 (90%) 72 (53%) 18 (25%) 49 (46%) 53 (62%)
e_l_s




    FALSE 6 (3.0%) 19 (14%) 22 (31%) 36 (34%) 2 (2.4%)
    TRUE 195 (97%) 118 (86%) 50 (69%) 71 (66%) 83 (98%)
s_l_b




    FALSE 174 (87%) 127 (93%) 65 (90%) 89 (83%) 79 (93%)
    TRUE 27 (13%) 10 (7.3%) 7 (9.7%) 18 (17%) 6 (7.1%)
s_l_e




    FALSE 195 (97%) 118 (86%) 50 (69%) 72 (67%) 83 (98%)
    TRUE 6 (3.0%) 19 (14%) 22 (31%) 35 (33%) 2 (2.4%)
1 n (%)

Chromosome 10

chrom <- 10
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
9a4bd3e Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 162 (81%) 43 (31%) 12 (17%) 37 (35%) 29 (34%)
    TRUE 39 (19%) 94 (69%) 60 (83%) 70 (65%) 56 (66%)
b_e_e




    FALSE 196 (98%) 135 (99%) 70 (97%) 106 (99%) 85 (100%)
    TRUE 5 (2.5%) 2 (1.5%) 2 (2.8%) 1 (0.9%) 0 (0%)
b_l_s




    FALSE 19 (9.5%) 12 (8.8%) 10 (14%) 23 (21%) 3 (3.5%)
    TRUE 182 (91%) 125 (91%) 62 (86%) 84 (79%) 82 (96%)
e_l_b




    FALSE 44 (22%) 96 (70%) 62 (86%) 71 (66%) 56 (66%)
    TRUE 157 (78%) 41 (30%) 10 (14%) 36 (34%) 29 (34%)
e_l_s




    FALSE 8 (4.0%) 43 (31%) 32 (44%) 40 (37%) 14 (16%)
    TRUE 193 (96%) 94 (69%) 40 (56%) 67 (63%) 71 (84%)
s_l_b




    FALSE 182 (91%) 128 (93%) 62 (86%) 86 (80%) 82 (96%)
    TRUE 19 (9.5%) 9 (6.6%) 10 (14%) 21 (20%) 3 (3.5%)
s_l_e




    FALSE 193 (96%) 94 (69%) 41 (57%) 70 (65%) 71 (84%)
    TRUE 8 (4.0%) 43 (31%) 31 (43%) 37 (35%) 14 (16%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 183 (91%) 68 (50%) 21 (29%) 43 (40%) 39 (46%)
    TRUE 18 (9.0%) 69 (50%) 51 (71%) 64 (60%) 46 (54%)
b_e_e




    FALSE 199 (99%) 137 (100%) 71 (99%) 107 (100%) 83 (98%)
    TRUE 2 (1.0%) 0 (0%) 1 (1.4%) 0 (0%) 2 (2.4%)
b_l_s




    FALSE 19 (9.5%) 17 (12%) 4 (5.6%) 18 (17%) 5 (5.9%)
    TRUE 182 (91%) 120 (88%) 68 (94%) 89 (83%) 80 (94%)
e_l_b




    FALSE 20 (10.0%) 69 (50%) 52 (72%) 64 (60%) 48 (56%)
    TRUE 181 (90%) 68 (50%) 20 (28%) 43 (40%) 37 (44%)
e_l_s




    FALSE 2 (1.0%) 26 (19%) 25 (35%) 28 (26%) 9 (11%)
    TRUE 199 (99%) 111 (81%) 47 (65%) 79 (74%) 76 (89%)
s_l_b




    FALSE 182 (91%) 123 (90%) 68 (94%) 89 (83%) 80 (94%)
    TRUE 19 (9.5%) 14 (10%) 4 (5.6%) 18 (17%) 5 (5.9%)
s_l_e




    FALSE 199 (99%) 111 (81%) 48 (67%) 79 (74%) 76 (89%)
    TRUE 2 (1.0%) 26 (19%) 24 (33%) 28 (26%) 9 (11%)
1 n (%)

Chromosome 11

chrom <- 10
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
ec0ba0b Andy Beck 2024-05-29
9a4bd3e Andy Beck 2024-05-29
34c040a Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
ec0ba0b Andy Beck 2024-05-29
9a4bd3e Andy Beck 2024-05-29
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 162 (81%) 43 (31%) 12 (17%) 37 (35%) 29 (34%)
    TRUE 39 (19%) 94 (69%) 60 (83%) 70 (65%) 56 (66%)
b_e_e




    FALSE 196 (98%) 135 (99%) 70 (97%) 106 (99%) 85 (100%)
    TRUE 5 (2.5%) 2 (1.5%) 2 (2.8%) 1 (0.9%) 0 (0%)
b_l_s




    FALSE 19 (9.5%) 12 (8.8%) 10 (14%) 23 (21%) 3 (3.5%)
    TRUE 182 (91%) 125 (91%) 62 (86%) 84 (79%) 82 (96%)
e_l_b




    FALSE 44 (22%) 96 (70%) 62 (86%) 71 (66%) 56 (66%)
    TRUE 157 (78%) 41 (30%) 10 (14%) 36 (34%) 29 (34%)
e_l_s




    FALSE 8 (4.0%) 43 (31%) 32 (44%) 40 (37%) 14 (16%)
    TRUE 193 (96%) 94 (69%) 40 (56%) 67 (63%) 71 (84%)
s_l_b




    FALSE 182 (91%) 128 (93%) 62 (86%) 86 (80%) 82 (96%)
    TRUE 19 (9.5%) 9 (6.6%) 10 (14%) 21 (20%) 3 (3.5%)
s_l_e




    FALSE 193 (96%) 94 (69%) 41 (57%) 70 (65%) 71 (84%)
    TRUE 8 (4.0%) 43 (31%) 31 (43%) 37 (35%) 14 (16%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 183 (91%) 68 (50%) 21 (29%) 43 (40%) 39 (46%)
    TRUE 18 (9.0%) 69 (50%) 51 (71%) 64 (60%) 46 (54%)
b_e_e




    FALSE 199 (99%) 137 (100%) 71 (99%) 107 (100%) 83 (98%)
    TRUE 2 (1.0%) 0 (0%) 1 (1.4%) 0 (0%) 2 (2.4%)
b_l_s




    FALSE 19 (9.5%) 17 (12%) 4 (5.6%) 18 (17%) 5 (5.9%)
    TRUE 182 (91%) 120 (88%) 68 (94%) 89 (83%) 80 (94%)
e_l_b




    FALSE 20 (10.0%) 69 (50%) 52 (72%) 64 (60%) 48 (56%)
    TRUE 181 (90%) 68 (50%) 20 (28%) 43 (40%) 37 (44%)
e_l_s




    FALSE 2 (1.0%) 26 (19%) 25 (35%) 28 (26%) 9 (11%)
    TRUE 199 (99%) 111 (81%) 47 (65%) 79 (74%) 76 (89%)
s_l_b




    FALSE 182 (91%) 123 (90%) 68 (94%) 89 (83%) 80 (94%)
    TRUE 19 (9.5%) 14 (10%) 4 (5.6%) 18 (17%) 5 (5.9%)
s_l_e




    FALSE 199 (99%) 111 (81%) 48 (67%) 79 (74%) 76 (89%)
    TRUE 2 (1.0%) 26 (19%) 24 (33%) 28 (26%) 9 (11%)
1 n (%)

Chromosome 12

chrom <- 12
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
76e67f9 Andy Beck 2024-06-26
292c663 Andy Beck 2024-06-13
ec0ba0b Andy Beck 2024-05-29
9a4bd3e Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
1243aea Andy Beck 2024-07-03
76e67f9 Andy Beck 2024-06-26
292c663 Andy Beck 2024-06-13
ec0ba0b Andy Beck 2024-05-29
9a4bd3e Andy Beck 2024-05-29
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 179 (89%) 52 (38%) 12 (17%) 38 (36%) 43 (51%)
    TRUE 22 (11%) 85 (62%) 60 (83%) 69 (64%) 42 (49%)
b_e_e




    FALSE 200 (100%) 135 (99%) 71 (99%) 105 (98%) 85 (100%)
    TRUE 1 (0.5%) 2 (1.5%) 1 (1.4%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 29 (14%) 10 (7.3%) 9 (13%) 13 (12%) 5 (5.9%)
    TRUE 172 (86%) 127 (93%) 63 (88%) 94 (88%) 80 (94%)
e_l_b




    FALSE 23 (11%) 87 (64%) 61 (85%) 71 (66%) 42 (49%)
    TRUE 178 (89%) 50 (36%) 11 (15%) 36 (34%) 43 (51%)
e_l_s




    FALSE 8 (4.0%) 30 (22%) 27 (38%) 35 (33%) 9 (11%)
    TRUE 193 (96%) 107 (78%) 45 (63%) 72 (67%) 76 (89%)
s_l_b




    FALSE 174 (87%) 128 (93%) 63 (88%) 95 (89%) 80 (94%)
    TRUE 27 (13%) 9 (6.6%) 9 (13%) 12 (11%) 5 (5.9%)
s_l_e




    FALSE 194 (97%) 108 (79%) 47 (65%) 72 (67%) 77 (91%)
    TRUE 7 (3.5%) 29 (21%) 25 (35%) 35 (33%) 8 (9.4%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 190 (95%) 65 (47%) 23 (32%) 53 (50%) 59 (69%)
    TRUE 11 (5.5%) 72 (53%) 49 (68%) 54 (50%) 26 (31%)
b_e_e




    FALSE 201 (100%) 134 (98%) 71 (99%) 102 (95%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 1 (1.4%) 5 (4.7%) 0 (0%)
b_l_s




    FALSE 15 (7.5%) 10 (7.3%) 8 (11%) 10 (9.3%) 5 (5.9%)
    TRUE 186 (93%) 127 (93%) 64 (89%) 97 (91%) 80 (94%)
e_l_b




    FALSE 11 (5.5%) 75 (55%) 50 (69%) 59 (55%) 26 (31%)
    TRUE 190 (95%) 62 (45%) 22 (31%) 48 (45%) 59 (69%)
e_l_s




    FALSE 1 (0.5%) 19 (14%) 17 (24%) 20 (19%) 3 (3.5%)
    TRUE 200 (100%) 118 (86%) 55 (76%) 87 (81%) 82 (96%)
s_l_b




    FALSE 189 (94%) 129 (94%) 65 (90%) 98 (92%) 80 (94%)
    TRUE 12 (6.0%) 8 (5.8%) 7 (9.7%) 9 (8.4%) 5 (5.9%)
s_l_e




    FALSE 200 (100%) 119 (87%) 55 (76%) 87 (81%) 82 (96%)
    TRUE 1 (0.5%) 18 (13%) 17 (24%) 20 (19%) 3 (3.5%)
1 n (%)

Chromosome 13

chrom <- 13
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
76e67f9 Andy Beck 2024-06-26
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
34c040a Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
1243aea Andy Beck 2024-07-03
76e67f9 Andy Beck 2024-06-26
292c663 Andy Beck 2024-06-13
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
fc667bc theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 162 (81%) 55 (40%) 12 (17%) 36 (34%) 33 (39%)
    TRUE 39 (19%) 82 (60%) 60 (83%) 71 (66%) 52 (61%)
b_e_e




    FALSE 200 (100%) 135 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 1 (0.5%) 2 (1.5%) 0 (0%) 0 (0%) 0 (0%)
b_l_s




    FALSE 24 (12%) 14 (10%) 14 (19%) 25 (23%) 8 (9.4%)
    TRUE 177 (88%) 123 (90%) 58 (81%) 82 (77%) 77 (91%)
e_l_b




    FALSE 40 (20%) 84 (61%) 60 (83%) 71 (66%) 52 (61%)
    TRUE 161 (80%) 53 (39%) 12 (17%) 36 (34%) 33 (39%)
e_l_s




    FALSE 8 (4.0%) 38 (28%) 41 (57%) 47 (44%) 15 (18%)
    TRUE 193 (96%) 99 (72%) 31 (43%) 60 (56%) 70 (82%)
s_l_b




    FALSE 178 (89%) 123 (90%) 59 (82%) 84 (79%) 78 (92%)
    TRUE 23 (11%) 14 (10%) 13 (18%) 23 (21%) 7 (8.2%)
s_l_e




    FALSE 193 (96%) 100 (73%) 33 (46%) 63 (59%) 72 (85%)
    TRUE 8 (4.0%) 37 (27%) 39 (54%) 44 (41%) 13 (15%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 179 (89%) 80 (58%) 19 (26%) 53 (50%) 41 (48%)
    TRUE 22 (11%) 57 (42%) 53 (74%) 54 (50%) 44 (52%)
b_e_e




    FALSE 200 (100%) 136 (99%) 71 (99%) 104 (97%) 83 (98%)
    TRUE 1 (0.5%) 1 (0.7%) 1 (1.4%) 3 (2.8%) 2 (2.4%)
b_l_s




    FALSE 23 (11%) 11 (8.0%) 11 (15%) 20 (19%) 9 (11%)
    TRUE 178 (89%) 126 (92%) 61 (85%) 87 (81%) 76 (89%)
e_l_b




    FALSE 23 (11%) 58 (42%) 54 (75%) 57 (53%) 46 (54%)
    TRUE 178 (89%) 79 (58%) 18 (25%) 50 (47%) 39 (46%)
e_l_s




    FALSE 3 (1.5%) 27 (20%) 27 (38%) 27 (25%) 10 (12%)
    TRUE 198 (99%) 110 (80%) 45 (63%) 80 (75%) 75 (88%)
s_l_b




    FALSE 181 (90%) 128 (93%) 61 (85%) 88 (82%) 76 (89%)
    TRUE 20 (10.0%) 9 (6.6%) 11 (15%) 19 (18%) 9 (11%)
s_l_e




    FALSE 198 (99%) 112 (82%) 45 (63%) 82 (77%) 76 (89%)
    TRUE 3 (1.5%) 25 (18%) 27 (38%) 25 (23%) 9 (11%)
1 n (%)

Chromosome 14

chrom <- 14
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
34c040a Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 159 (79%) 52 (38%) 11 (15%) 36 (34%) 32 (38%)
    TRUE 42 (21%) 85 (62%) 61 (85%) 71 (66%) 53 (62%)
b_e_e




    FALSE 200 (100%) 136 (99%) 72 (100%) 103 (96%) 83 (98%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 4 (3.7%) 2 (2.4%)
b_l_s




    FALSE 28 (14%) 24 (18%) 9 (13%) 25 (23%) 6 (7.1%)
    TRUE 173 (86%) 113 (82%) 63 (88%) 82 (77%) 79 (93%)
e_l_b




    FALSE 43 (21%) 86 (63%) 61 (85%) 75 (70%) 55 (65%)
    TRUE 158 (79%) 51 (37%) 11 (15%) 32 (30%) 30 (35%)
e_l_s




    FALSE 8 (4.0%) 45 (33%) 37 (51%) 42 (39%) 12 (14%)
    TRUE 193 (96%) 92 (67%) 35 (49%) 65 (61%) 73 (86%)
s_l_b




    FALSE 176 (88%) 114 (83%) 64 (89%) 84 (79%) 80 (94%)
    TRUE 25 (12%) 23 (17%) 8 (11%) 23 (21%) 5 (5.9%)
s_l_e




    FALSE 193 (96%) 93 (68%) 35 (49%) 67 (63%) 74 (87%)
    TRUE 8 (4.0%) 44 (32%) 37 (51%) 40 (37%) 11 (13%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 165 (82%) 66 (48%) 21 (29%) 41 (38%) 45 (53%)
    TRUE 36 (18%) 71 (52%) 51 (71%) 66 (62%) 40 (47%)
b_e_e




    FALSE 199 (99%) 131 (96%) 72 (100%) 105 (98%) 85 (100%)
    TRUE 2 (1.0%) 6 (4.4%) 0 (0%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 23 (11%) 12 (8.8%) 6 (8.3%) 16 (15%) 3 (3.5%)
    TRUE 178 (89%) 125 (91%) 66 (92%) 91 (85%) 82 (96%)
e_l_b




    FALSE 38 (19%) 77 (56%) 51 (71%) 68 (64%) 40 (47%)
    TRUE 163 (81%) 60 (44%) 21 (29%) 39 (36%) 45 (53%)
e_l_s




    FALSE 8 (4.0%) 24 (18%) 29 (40%) 31 (29%) 7 (8.2%)
    TRUE 193 (96%) 113 (82%) 43 (60%) 76 (71%) 78 (92%)
s_l_b




    FALSE 178 (89%) 126 (92%) 66 (92%) 92 (86%) 82 (96%)
    TRUE 23 (11%) 11 (8.0%) 6 (8.3%) 15 (14%) 3 (3.5%)
s_l_e




    FALSE 195 (97%) 113 (82%) 44 (61%) 76 (71%) 78 (92%)
    TRUE 6 (3.0%) 24 (18%) 28 (39%) 31 (29%) 7 (8.2%)
1 n (%)

Chromosome 15

chrom <- 15
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
34c040a Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 140 (70%) 50 (36%) 12 (17%) 35 (33%) 42 (49%)
    TRUE 61 (30%) 87 (64%) 60 (83%) 72 (67%) 43 (51%)
b_e_e




    FALSE 198 (99%) 137 (100%) 71 (99%) 103 (96%) 83 (98%)
    TRUE 3 (1.5%) 0 (0%) 1 (1.4%) 4 (3.7%) 2 (2.4%)
b_l_s




    FALSE 27 (13%) 13 (9.5%) 18 (25%) 28 (26%) 8 (9.4%)
    TRUE 174 (87%) 124 (91%) 54 (75%) 79 (74%) 77 (91%)
e_l_b




    FALSE 64 (32%) 87 (64%) 61 (85%) 76 (71%) 45 (53%)
    TRUE 137 (68%) 50 (36%) 11 (15%) 31 (29%) 40 (47%)
e_l_s




    FALSE 22 (11%) 36 (26%) 31 (43%) 48 (45%) 17 (20%)
    TRUE 179 (89%) 101 (74%) 41 (57%) 59 (55%) 68 (80%)
s_l_b




    FALSE 175 (87%) 124 (91%) 56 (78%) 81 (76%) 77 (91%)
    TRUE 26 (13%) 13 (9.5%) 16 (22%) 26 (24%) 8 (9.4%)
s_l_e




    FALSE 180 (90%) 103 (75%) 42 (58%) 62 (58%) 70 (82%)
    TRUE 21 (10%) 34 (25%) 30 (42%) 45 (42%) 15 (18%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 153 (76%) 68 (50%) 27 (38%) 51 (48%) 32 (38%)
    TRUE 48 (24%) 69 (50%) 45 (63%) 56 (52%) 53 (62%)
b_e_e




    FALSE 198 (99%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 3 (1.5%) 0 (0%) 0 (0%) 0 (0%) 0 (0%)
b_l_s




    FALSE 20 (10.0%) 14 (10%) 14 (19%) 26 (24%) 4 (4.7%)
    TRUE 181 (90%) 123 (90%) 58 (81%) 81 (76%) 81 (95%)
e_l_b




    FALSE 51 (25%) 69 (50%) 45 (63%) 56 (52%) 53 (62%)
    TRUE 150 (75%) 68 (50%) 27 (38%) 51 (48%) 32 (38%)
e_l_s




    FALSE 14 (7.0%) 28 (20%) 20 (28%) 34 (32%) 12 (14%)
    TRUE 187 (93%) 109 (80%) 52 (72%) 73 (68%) 73 (86%)
s_l_b




    FALSE 182 (91%) 124 (91%) 59 (82%) 82 (77%) 81 (95%)
    TRUE 19 (9.5%) 13 (9.5%) 13 (18%) 25 (23%) 4 (4.7%)
s_l_e




    FALSE 188 (94%) 110 (80%) 53 (74%) 74 (69%) 75 (88%)
    TRUE 13 (6.5%) 27 (20%) 19 (26%) 33 (31%) 10 (12%)
1 n (%)

Chromosome 16

chrom <- 16
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
01d26a4 theandyb 2025-06-18
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 146 (73%) 60 (44%) 18 (25%) 24 (22%) 38 (45%)
    TRUE 55 (27%) 77 (56%) 54 (75%) 83 (78%) 47 (55%)
b_e_e




    FALSE 199 (99%) 136 (99%) 72 (100%) 107 (100%) 81 (95%)
    TRUE 2 (1.0%) 1 (0.7%) 0 (0%) 0 (0%) 4 (4.7%)
b_l_s




    FALSE 28 (14%) 15 (11%) 10 (14%) 18 (17%) 7 (8.2%)
    TRUE 173 (86%) 122 (89%) 62 (86%) 89 (83%) 78 (92%)
e_l_b




    FALSE 57 (28%) 78 (57%) 54 (75%) 83 (78%) 51 (60%)
    TRUE 144 (72%) 59 (43%) 18 (25%) 24 (22%) 34 (40%)
e_l_s




    FALSE 15 (7.5%) 31 (23%) 32 (44%) 45 (42%) 14 (16%)
    TRUE 186 (93%) 106 (77%) 40 (56%) 62 (58%) 71 (84%)
s_l_b




    FALSE 175 (87%) 122 (89%) 63 (88%) 89 (83%) 78 (92%)
    TRUE 26 (13%) 15 (11%) 9 (13%) 18 (17%) 7 (8.2%)
s_l_e




    FALSE 187 (93%) 107 (78%) 42 (58%) 63 (59%) 72 (85%)
    TRUE 14 (7.0%) 30 (22%) 30 (42%) 44 (41%) 13 (15%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 155 (77%) 71 (52%) 24 (33%) 41 (38%) 52 (61%)
    TRUE 46 (23%) 66 (48%) 48 (67%) 66 (62%) 33 (39%)
b_e_e




    FALSE 200 (100%) 136 (99%) 72 (100%) 104 (97%) 85 (100%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 3 (2.8%) 0 (0%)
b_l_s




    FALSE 23 (11%) 14 (10%) 13 (18%) 18 (17%) 9 (11%)
    TRUE 178 (89%) 123 (90%) 59 (82%) 89 (83%) 76 (89%)
e_l_b




    FALSE 47 (23%) 67 (49%) 48 (67%) 69 (64%) 33 (39%)
    TRUE 154 (77%) 70 (51%) 24 (33%) 38 (36%) 52 (61%)
e_l_s




    FALSE 13 (6.5%) 19 (14%) 25 (35%) 35 (33%) 6 (7.1%)
    TRUE 188 (94%) 118 (86%) 47 (65%) 72 (67%) 79 (93%)
s_l_b




    FALSE 180 (90%) 124 (91%) 59 (82%) 91 (85%) 77 (91%)
    TRUE 21 (10%) 13 (9.5%) 13 (18%) 16 (15%) 8 (9.4%)
s_l_e




    FALSE 188 (94%) 122 (89%) 47 (65%) 73 (68%) 79 (93%)
    TRUE 13 (6.5%) 15 (11%) 25 (35%) 34 (32%) 6 (7.1%)
1 n (%)

Chromosome 17

chrom <- 17
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
34c040a Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 151 (75%) 55 (40%) 13 (18%) 35 (33%) 27 (32%)
    TRUE 50 (25%) 82 (60%) 59 (82%) 72 (67%) 58 (68%)
b_e_e




    FALSE 196 (98%) 133 (97%) 72 (100%) 105 (98%) 83 (98%)
    TRUE 5 (2.5%) 4 (2.9%) 0 (0%) 2 (1.9%) 2 (2.4%)
b_l_s




    FALSE 35 (17%) 20 (15%) 13 (18%) 28 (26%) 12 (14%)
    TRUE 166 (83%) 117 (85%) 59 (82%) 79 (74%) 73 (86%)
e_l_b




    FALSE 55 (27%) 86 (63%) 59 (82%) 74 (69%) 60 (71%)
    TRUE 146 (73%) 51 (37%) 13 (18%) 33 (31%) 25 (29%)
e_l_s




    FALSE 27 (13%) 44 (32%) 42 (58%) 53 (50%) 22 (26%)
    TRUE 174 (87%) 93 (68%) 30 (42%) 54 (50%) 63 (74%)
s_l_b




    FALSE 168 (84%) 118 (86%) 60 (83%) 80 (75%) 73 (86%)
    TRUE 33 (16%) 19 (14%) 12 (17%) 27 (25%) 12 (14%)
s_l_e




    FALSE 174 (87%) 95 (69%) 32 (44%) 57 (53%) 63 (74%)
    TRUE 27 (13%) 42 (31%) 40 (56%) 50 (47%) 22 (26%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 146 (73%) 69 (50%) 25 (35%) 43 (40%) 36 (42%)
    TRUE 55 (27%) 68 (50%) 47 (65%) 64 (60%) 49 (58%)
b_e_e




    FALSE 200 (100%) 136 (99%) 70 (97%) 103 (96%) 84 (99%)
    TRUE 1 (0.5%) 1 (0.7%) 2 (2.8%) 4 (3.7%) 1 (1.2%)
b_l_s




    FALSE 34 (17%) 18 (13%) 12 (17%) 24 (22%) 14 (16%)
    TRUE 167 (83%) 119 (87%) 60 (83%) 83 (78%) 71 (84%)
e_l_b




    FALSE 56 (28%) 69 (50%) 49 (68%) 68 (64%) 50 (59%)
    TRUE 145 (72%) 68 (50%) 23 (32%) 39 (36%) 35 (41%)
e_l_s




    FALSE 12 (6.0%) 31 (23%) 27 (38%) 35 (33%) 21 (25%)
    TRUE 189 (94%) 106 (77%) 45 (63%) 72 (67%) 64 (75%)
s_l_b




    FALSE 172 (86%) 120 (88%) 61 (85%) 84 (79%) 71 (84%)
    TRUE 29 (14%) 17 (12%) 11 (15%) 23 (21%) 14 (16%)
s_l_e




    FALSE 189 (94%) 107 (78%) 46 (64%) 74 (69%) 64 (75%)
    TRUE 12 (6.0%) 30 (22%) 26 (36%) 33 (31%) 21 (25%)
1 n (%)

Chromosome 18

chrom <- 18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
d6dca59 Andy Beck 2024-05-29
8041a90 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 164 (82%) 66 (48%) 17 (24%) 40 (37%) 41 (48%)
    TRUE 37 (18%) 71 (52%) 55 (76%) 67 (63%) 44 (52%)
b_e_e




    FALSE 197 (98%) 133 (97%) 71 (99%) 104 (97%) 82 (96%)
    TRUE 4 (2.0%) 4 (2.9%) 1 (1.4%) 3 (2.8%) 3 (3.5%)
b_l_s




    FALSE 28 (14%) 20 (15%) 11 (15%) 32 (30%) 5 (5.9%)
    TRUE 173 (86%) 117 (85%) 61 (85%) 75 (70%) 80 (94%)
e_l_b




    FALSE 41 (20%) 75 (55%) 56 (78%) 70 (65%) 47 (55%)
    TRUE 160 (80%) 62 (45%) 16 (22%) 37 (35%) 38 (45%)
e_l_s




    FALSE 11 (5.5%) 25 (18%) 28 (39%) 47 (44%) 18 (21%)
    TRUE 190 (95%) 112 (82%) 44 (61%) 60 (56%) 67 (79%)
s_l_b




    FALSE 174 (87%) 118 (86%) 64 (89%) 77 (72%) 80 (94%)
    TRUE 27 (13%) 19 (14%) 8 (11%) 30 (28%) 5 (5.9%)
s_l_e




    FALSE 191 (95%) 115 (84%) 45 (63%) 62 (58%) 67 (79%)
    TRUE 10 (5.0%) 22 (16%) 27 (38%) 45 (42%) 18 (21%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 169 (84%) 85 (62%) 17 (24%) 39 (36%) 45 (53%)
    TRUE 32 (16%) 52 (38%) 55 (76%) 68 (64%) 40 (47%)
b_e_e




    FALSE 199 (99%) 134 (98%) 71 (99%) 104 (97%) 83 (98%)
    TRUE 2 (1.0%) 3 (2.2%) 1 (1.4%) 3 (2.8%) 2 (2.4%)
b_l_s




    FALSE 20 (10.0%) 12 (8.8%) 12 (17%) 23 (21%) 7 (8.2%)
    TRUE 181 (90%) 125 (91%) 60 (83%) 84 (79%) 78 (92%)
e_l_b




    FALSE 34 (17%) 55 (40%) 56 (78%) 71 (66%) 42 (49%)
    TRUE 167 (83%) 82 (60%) 16 (22%) 36 (34%) 43 (51%)
e_l_s




    FALSE 6 (3.0%) 21 (15%) 27 (38%) 31 (29%) 13 (15%)
    TRUE 195 (97%) 116 (85%) 45 (63%) 76 (71%) 72 (85%)
s_l_b




    FALSE 183 (91%) 126 (92%) 60 (83%) 87 (81%) 78 (92%)
    TRUE 18 (9.0%) 11 (8.0%) 12 (17%) 20 (19%) 7 (8.2%)
s_l_e




    FALSE 195 (97%) 116 (85%) 46 (64%) 76 (71%) 72 (85%)
    TRUE 6 (3.0%) 21 (15%) 26 (36%) 31 (29%) 13 (15%)
1 n (%)

Chromosome 19

chrom <- 19
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
cd54733 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 107 (53%) 44 (32%) 24 (33%) 32 (30%) 36 (42%)
    TRUE 94 (47%) 93 (68%) 48 (67%) 75 (70%) 49 (58%)
b_e_e




    FALSE 199 (99%) 133 (97%) 71 (99%) 105 (98%) 84 (99%)
    TRUE 2 (1.0%) 4 (2.9%) 1 (1.4%) 2 (1.9%) 1 (1.2%)
b_l_s




    FALSE 49 (24%) 25 (18%) 21 (29%) 33 (31%) 12 (14%)
    TRUE 152 (76%) 112 (82%) 51 (71%) 74 (69%) 73 (86%)
e_l_b




    FALSE 96 (48%) 97 (71%) 49 (68%) 77 (72%) 50 (59%)
    TRUE 105 (52%) 40 (29%) 23 (32%) 30 (28%) 35 (41%)
e_l_s




    FALSE 53 (26%) 54 (39%) 32 (44%) 53 (50%) 24 (28%)
    TRUE 148 (74%) 83 (61%) 40 (56%) 54 (50%) 61 (72%)
s_l_b




    FALSE 155 (77%) 113 (82%) 52 (72%) 78 (73%) 73 (86%)
    TRUE 46 (23%) 24 (18%) 20 (28%) 29 (27%) 12 (14%)
s_l_e




    FALSE 151 (75%) 87 (64%) 40 (56%) 55 (51%) 63 (74%)
    TRUE 50 (25%) 50 (36%) 32 (44%) 52 (49%) 22 (26%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 143 (71%) 52 (38%) 31 (43%) 51 (48%) 48 (56%)
    TRUE 58 (29%) 85 (62%) 41 (57%) 56 (52%) 37 (44%)
b_e_e




    FALSE 199 (99%) 134 (98%) 72 (100%) 106 (99%) 84 (99%)
    TRUE 2 (1.0%) 3 (2.2%) 0 (0%) 1 (0.9%) 1 (1.2%)
b_l_s




    FALSE 42 (21%) 24 (18%) 20 (28%) 36 (34%) 9 (11%)
    TRUE 159 (79%) 113 (82%) 52 (72%) 71 (66%) 76 (89%)
e_l_b




    FALSE 60 (30%) 88 (64%) 41 (57%) 57 (53%) 38 (45%)
    TRUE 141 (70%) 49 (36%) 31 (43%) 50 (47%) 47 (55%)
e_l_s




    FALSE 32 (16%) 41 (30%) 26 (36%) 43 (40%) 6 (7.1%)
    TRUE 169 (84%) 96 (70%) 46 (64%) 64 (60%) 79 (93%)
s_l_b




    FALSE 161 (80%) 114 (83%) 52 (72%) 76 (71%) 77 (91%)
    TRUE 40 (20%) 23 (17%) 20 (28%) 31 (29%) 8 (9.4%)
s_l_e




    FALSE 174 (87%) 99 (72%) 46 (64%) 65 (61%) 79 (93%)
    TRUE 27 (13%) 38 (28%) 26 (36%) 42 (39%) 6 (7.1%)
1 n (%)

Chromosome 20

chrom <- 20
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
cd54733 Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 141 (70%) 59 (43%) 22 (31%) 34 (32%) 39 (46%)
    TRUE 60 (30%) 78 (57%) 50 (69%) 73 (68%) 46 (54%)
b_e_e




    FALSE 197 (98%) 136 (99%) 72 (100%) 106 (99%) 83 (98%)
    TRUE 4 (2.0%) 1 (0.7%) 0 (0%) 1 (0.9%) 2 (2.4%)
b_l_s




    FALSE 57 (28%) 25 (18%) 15 (21%) 21 (20%) 17 (20%)
    TRUE 144 (72%) 112 (82%) 57 (79%) 86 (80%) 68 (80%)
e_l_b




    FALSE 64 (32%) 79 (58%) 50 (69%) 74 (69%) 48 (56%)
    TRUE 137 (68%) 58 (42%) 22 (31%) 33 (31%) 37 (44%)
e_l_s




    FALSE 37 (18%) 43 (31%) 31 (43%) 46 (43%) 23 (27%)
    TRUE 164 (82%) 94 (69%) 41 (57%) 61 (57%) 62 (73%)
s_l_b




    FALSE 148 (74%) 115 (84%) 59 (82%) 88 (82%) 69 (81%)
    TRUE 53 (26%) 22 (16%) 13 (18%) 19 (18%) 16 (19%)
s_l_e




    FALSE 167 (83%) 97 (71%) 43 (60%) 63 (59%) 62 (73%)
    TRUE 34 (17%) 40 (29%) 29 (40%) 44 (41%) 23 (27%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 151 (75%) 59 (43%) 23 (32%) 37 (35%) 44 (52%)
    TRUE 50 (25%) 78 (57%) 49 (68%) 70 (65%) 41 (48%)
b_e_e




    FALSE 197 (98%) 134 (98%) 71 (99%) 103 (96%) 85 (100%)
    TRUE 4 (2.0%) 3 (2.2%) 1 (1.4%) 4 (3.7%) 0 (0%)
b_l_s




    FALSE 49 (24%) 22 (16%) 16 (22%) 31 (29%) 16 (19%)
    TRUE 152 (76%) 115 (84%) 56 (78%) 76 (71%) 69 (81%)
e_l_b




    FALSE 54 (27%) 81 (59%) 50 (69%) 74 (69%) 41 (48%)
    TRUE 147 (73%) 56 (41%) 22 (31%) 33 (31%) 44 (52%)
e_l_s




    FALSE 27 (13%) 33 (24%) 27 (38%) 43 (40%) 18 (21%)
    TRUE 174 (87%) 104 (76%) 45 (63%) 64 (60%) 67 (79%)
s_l_b




    FALSE 154 (77%) 116 (85%) 58 (81%) 77 (72%) 70 (82%)
    TRUE 47 (23%) 21 (15%) 14 (19%) 30 (28%) 15 (18%)
s_l_e




    FALSE 180 (90%) 105 (77%) 46 (64%) 64 (60%) 68 (80%)
    TRUE 21 (10%) 32 (23%) 26 (36%) 43 (40%) 17 (20%)
1 n (%)

Chromosome 21

chrom <- 21
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 112 (56%) 44 (32%) 19 (26%) 35 (33%) 33 (39%)
    TRUE 89 (44%) 93 (68%) 53 (74%) 72 (67%) 52 (61%)
b_e_e




    FALSE 200 (100%) 133 (97%) 71 (99%) 102 (95%) 81 (95%)
    TRUE 1 (0.5%) 4 (2.9%) 1 (1.4%) 5 (4.7%) 4 (4.7%)
b_l_s




    FALSE 40 (20%) 18 (13%) 22 (31%) 32 (30%) 14 (16%)
    TRUE 161 (80%) 119 (87%) 50 (69%) 75 (70%) 71 (84%)
e_l_b




    FALSE 90 (45%) 97 (71%) 54 (75%) 77 (72%) 56 (66%)
    TRUE 111 (55%) 40 (29%) 18 (25%) 30 (28%) 29 (34%)
e_l_s




    FALSE 45 (22%) 56 (41%) 37 (51%) 47 (44%) 27 (32%)
    TRUE 156 (78%) 81 (59%) 35 (49%) 60 (56%) 58 (68%)
s_l_b




    FALSE 166 (83%) 122 (89%) 51 (71%) 79 (74%) 71 (84%)
    TRUE 35 (17%) 15 (11%) 21 (29%) 28 (26%) 14 (16%)
s_l_e




    FALSE 158 (79%) 84 (61%) 36 (50%) 61 (57%) 60 (71%)
    TRUE 43 (21%) 53 (39%) 36 (50%) 46 (43%) 25 (29%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 147 (73%) 54 (39%) 26 (36%) 47 (44%) 40 (47%)
    TRUE 54 (27%) 83 (61%) 46 (64%) 60 (56%) 45 (53%)
b_e_e




    FALSE 196 (98%) 133 (97%) 72 (100%) 103 (96%) 83 (98%)
    TRUE 5 (2.5%) 4 (2.9%) 0 (0%) 4 (3.7%) 2 (2.4%)
b_l_s




    FALSE 33 (16%) 26 (19%) 19 (26%) 20 (19%) 13 (15%)
    TRUE 168 (84%) 111 (81%) 53 (74%) 87 (81%) 72 (85%)
e_l_b




    FALSE 59 (29%) 87 (64%) 46 (64%) 64 (60%) 47 (55%)
    TRUE 142 (71%) 50 (36%) 26 (36%) 43 (40%) 38 (45%)
e_l_s




    FALSE 23 (11%) 41 (30%) 32 (44%) 44 (41%) 20 (24%)
    TRUE 178 (89%) 96 (70%) 40 (56%) 63 (59%) 65 (76%)
s_l_b




    FALSE 169 (84%) 113 (82%) 53 (74%) 90 (84%) 73 (86%)
    TRUE 32 (16%) 24 (18%) 19 (26%) 17 (16%) 12 (14%)
s_l_e




    FALSE 180 (90%) 99 (72%) 41 (57%) 68 (64%) 66 (78%)
    TRUE 21 (10%) 38 (28%) 31 (43%) 39 (36%) 19 (22%)
1 n (%)

Chromosome 22

chrom <- 22
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

table_total_errors(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 113 (56%) 35 (26%) 15 (21%) 33 (31%) 28 (33%)
    TRUE 88 (44%) 102 (74%) 57 (79%) 74 (69%) 57 (67%)
b_e_e




    FALSE 197 (98%) 136 (99%) 72 (100%) 102 (95%) 84 (99%)
    TRUE 4 (2.0%) 1 (0.7%) 0 (0%) 5 (4.7%) 1 (1.2%)
b_l_s




    FALSE 62 (31%) 33 (24%) 19 (26%) 33 (31%) 21 (25%)
    TRUE 139 (69%) 104 (76%) 53 (74%) 74 (69%) 64 (75%)
e_l_b




    FALSE 92 (46%) 103 (75%) 57 (79%) 79 (74%) 58 (68%)
    TRUE 109 (54%) 34 (25%) 15 (21%) 28 (26%) 27 (32%)
e_l_s




    FALSE 53 (26%) 66 (48%) 48 (67%) 54 (50%) 39 (46%)
    TRUE 148 (74%) 71 (52%) 24 (33%) 53 (50%) 46 (54%)
s_l_b




    FALSE 143 (71%) 108 (79%) 54 (75%) 76 (71%) 64 (75%)
    TRUE 58 (29%) 29 (21%) 18 (25%) 31 (29%) 21 (25%)
s_l_e




    FALSE 153 (76%) 74 (54%) 24 (33%) 56 (52%) 46 (54%)
    TRUE 48 (24%) 63 (46%) 48 (67%) 51 (48%) 39 (46%)
1 n (%)
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 118 (59%) 53 (39%) 20 (28%) 48 (45%) 36 (42%)
    TRUE 83 (41%) 84 (61%) 52 (72%) 59 (55%) 49 (58%)
b_e_e




    FALSE 198 (99%) 136 (99%) 71 (99%) 101 (94%) 82 (96%)
    TRUE 3 (1.5%) 1 (0.7%) 1 (1.4%) 6 (5.6%) 3 (3.5%)
b_l_s




    FALSE 58 (29%) 29 (21%) 21 (29%) 29 (27%) 12 (14%)
    TRUE 143 (71%) 108 (79%) 51 (71%) 78 (73%) 73 (86%)
e_l_b




    FALSE 86 (43%) 85 (62%) 53 (74%) 65 (61%) 52 (61%)
    TRUE 115 (57%) 52 (38%) 19 (26%) 42 (39%) 33 (39%)
e_l_s




    FALSE 61 (30%) 49 (36%) 38 (53%) 49 (46%) 23 (27%)
    TRUE 140 (70%) 88 (64%) 34 (47%) 58 (54%) 62 (73%)
s_l_b




    FALSE 146 (73%) 110 (80%) 52 (72%) 79 (74%) 74 (87%)
    TRUE 55 (27%) 27 (20%) 20 (28%) 28 (26%) 11 (13%)
s_l_e




    FALSE 144 (72%) 90 (66%) 34 (47%) 62 (58%) 66 (78%)
    TRUE 57 (28%) 47 (34%) 38 (53%) 45 (42%) 19 (22%)
1 n (%)

Chromosome X

plot_total_errors(df_switch_x, "Beagle", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
9a4bd3e Andy Beck 2024-05-29
plot_total_errors(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_errors(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
table_total_errors(df_switch_x, "pop")
Characteristic AFR
N = 200
1
AMR
N = 200
1
EAS
N = 200
1
EUR
N = 200
1
SAS
N = 200
1
b_l_e




    FALSE 1 (0.5%) 6 (3.0%) 1 (0.5%) 0 (0%) 1 (0.5%)
    TRUE 199 (100%) 194 (97%) 199 (100%) 200 (100%) 199 (100%)
b_e_e




    FALSE 200 (100%) 200 (100%) 200 (100%) 200 (100%) 200 (100%)
b_l_s




    FALSE 73 (37%) 63 (32%) 107 (54%) 80 (40%) 97 (49%)
    TRUE 127 (64%) 137 (69%) 93 (47%) 120 (60%) 103 (52%)
e_l_b




    FALSE 199 (100%) 194 (97%) 199 (100%) 200 (100%) 199 (100%)
    TRUE 1 (0.5%) 6 (3.0%) 1 (0.5%) 0 (0%) 1 (0.5%)
e_l_s




    FALSE 198 (99%) 188 (94%) 200 (100%) 198 (99%) 198 (99%)
    TRUE 2 (1.0%) 12 (6.0%) 0 (0%) 2 (1.0%) 2 (1.0%)
s_l_b




    FALSE 135 (68%) 141 (71%) 101 (51%) 127 (64%) 103 (52%)
    TRUE 65 (33%) 59 (30%) 99 (50%) 73 (37%) 97 (49%)
s_l_e




    FALSE 3 (1.5%) 14 (7.0%) 0 (0%) 2 (1.0%) 2 (1.0%)
    TRUE 197 (99%) 186 (93%) 200 (100%) 198 (99%) 198 (99%)
1 n (%)
cross_meth_plot(df_switch_x, "Total Errors", plot_total_errors, "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19

Error Rate

plot_total_rate <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
         Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
         SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Error Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_total_rate_noth <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_switch_b + n_flip_b) / n_het,
         Eagle = (n_switch_e + n_flip_e) / n_het,
         SHAPEIT = (n_switch_s + n_flip_s) / n_het) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Error Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

Chromosome 1

chrom <- 1 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 2

chrom <- 2
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 3

chrom <- 3
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
292c663 Andy Beck 2024-06-13
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 4

chrom <- 4
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 5

chrom <- 5
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 6

chrom <- 6
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 7

chrom <- 7
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 8

chrom <- 8
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 9

chrom <- 9
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 10

chrom <- 10
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
c2bd645 theandyb 2025-06-16
1243aea Andy Beck 2024-07-03
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 11

chrom <- 11
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 12

chrom <- 12
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 13

chrom <- 13
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 14

chrom <- 14
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 15

chrom <- 15
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 16

chrom <- 16
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 17

chrom <- 17
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 18

chrom <- 18
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 19

chrom <- 19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 20

chrom <- 20 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 21

chrom <- 21 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Chromosome X

plot_total_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_total_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
cross_meth_plot(df_switch_x, "Total Errors", plot_total_rate, "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19

Non-flip Switches

plot_switches <- function(df, m1, m2, pop, chrom=15){
  p <- df %>%
    mutate(Beagle = n_other_beagle,
         Eagle = n_other_eagle,
         SHAPEIT = n_other_shapeit) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switches", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_switches_noth <- function(df, m1, m2, pop, chrom=15){
  p <- df %>%
    mutate(Beagle = n_switch_b,
         Eagle = n_switch_e,
         SHAPEIT = n_switch_s) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switches", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

table_switches <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_other_beagle ),
         Eagle =  (n_other_eagle),
         SHAPEIT =  (n_other_shapeit)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

table_switches_noth <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_switch_b ),
         Eagle =  (n_switch_e),
         SHAPEIT =  (n_switch_s)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

Chromosome 1

chrom <- 1

plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 163 (81%) 81 (59%) 39 (54%) 72 (67%) 53 (62%)
    TRUE 38 (19%) 56 (41%) 33 (46%) 35 (33%) 32 (38%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 41 (20%) 58 (42%) 33 (46%) 37 (35%) 33 (39%)
    TRUE 160 (80%) 79 (58%) 39 (54%) 70 (65%) 52 (61%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 150 (75%) 78 (57%) 33 (46%) 72 (67%) 44 (52%)
    TRUE 51 (25%) 59 (43%) 39 (54%) 35 (33%) 41 (48%)
e_l_b




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
e_l_s




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
s_l_b




    FALSE 54 (27%) 61 (45%) 39 (54%) 39 (36%) 41 (48%)
    TRUE 147 (73%) 76 (55%) 33 (46%) 68 (64%) 44 (52%)
s_l_e




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 2

chrom <- 2
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 161 (80%) 78 (57%) 31 (43%) 65 (61%) 50 (59%)
    TRUE 40 (20%) 59 (43%) 41 (57%) 42 (39%) 35 (41%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 43 (21%) 62 (45%) 42 (58%) 43 (40%) 35 (41%)
    TRUE 158 (79%) 75 (55%) 30 (42%) 64 (60%) 50 (59%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 131 (65%) 75 (55%) 31 (43%) 70 (65%) 52 (61%)
    TRUE 70 (35%) 62 (45%) 41 (57%) 37 (35%) 33 (39%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 75 (37%) 65 (47%) 41 (57%) 39 (36%) 38 (45%)
    TRUE 126 (63%) 72 (53%) 31 (43%) 68 (64%) 47 (55%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 3

chrom <- 3
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 154 (77%) 75 (55%) 35 (49%) 76 (71%) 41 (48%)
    TRUE 47 (23%) 62 (45%) 37 (51%) 31 (29%) 44 (52%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 48 (24%) 65 (47%) 41 (57%) 34 (32%) 48 (56%)
    TRUE 153 (76%) 72 (53%) 31 (43%) 73 (68%) 37 (44%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 132 (66%) 68 (50%) 30 (42%) 61 (57%) 38 (45%)
    TRUE 69 (34%) 69 (50%) 42 (58%) 46 (43%) 47 (55%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 75 (37%) 72 (53%) 42 (58%) 49 (46%) 51 (60%)
    TRUE 126 (63%) 65 (47%) 30 (42%) 58 (54%) 34 (40%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 4

chrom <- 4
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 161 (80%) 77 (56%) 39 (54%) 76 (71%) 55 (65%)
    TRUE 40 (20%) 60 (44%) 33 (46%) 31 (29%) 30 (35%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 44 (22%) 62 (45%) 34 (47%) 32 (30%) 35 (41%)
    TRUE 157 (78%) 75 (55%) 38 (53%) 75 (70%) 50 (59%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 137 (68%) 62 (45%) 23 (32%) 67 (63%) 39 (46%)
    TRUE 64 (32%) 75 (55%) 49 (68%) 40 (37%) 46 (54%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
s_l_b




    FALSE 68 (34%) 77 (56%) 53 (74%) 43 (40%) 48 (56%)
    TRUE 133 (66%) 60 (44%) 19 (26%) 64 (60%) 37 (44%)
s_l_e




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 5

chrom <- 5
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 152 (76%) 77 (56%) 36 (50%) 67 (63%) 47 (55%)
    TRUE 49 (24%) 60 (44%) 36 (50%) 40 (37%) 38 (45%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 56 (28%) 64 (47%) 36 (50%) 42 (39%) 39 (46%)
    TRUE 145 (72%) 73 (53%) 36 (50%) 65 (61%) 46 (54%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 143 (71%) 59 (43%) 29 (40%) 68 (64%) 48 (56%)
    TRUE 58 (29%) 78 (57%) 43 (60%) 39 (36%) 37 (44%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 62 (31%) 80 (58%) 45 (63%) 43 (40%) 40 (47%)
    TRUE 139 (69%) 57 (42%) 27 (38%) 64 (60%) 45 (53%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 6

chrom <- 6
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 144 (72%) 84 (61%) 34 (47%) 68 (64%) 45 (53%)
    TRUE 57 (28%) 53 (39%) 38 (53%) 39 (36%) 40 (47%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 62 (31%) 55 (40%) 38 (53%) 44 (41%) 41 (48%)
    TRUE 139 (69%) 82 (60%) 34 (47%) 63 (59%) 44 (52%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 132 (66%) 69 (50%) 30 (42%) 72 (67%) 42 (49%)
    TRUE 69 (34%) 68 (50%) 42 (58%) 35 (33%) 43 (51%)
e_l_b




    FALSE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 0 (0%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
s_l_b




    FALSE 74 (37%) 69 (50%) 43 (60%) 37 (35%) 45 (53%)
    TRUE 127 (63%) 68 (50%) 29 (40%) 70 (65%) 40 (47%)
s_l_e




    FALSE 0 (0%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 7

chrom <- 7
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
b_l_s




    FALSE 172 (86%) 74 (54%) 31 (43%) 79 (74%) 47 (55%)
    TRUE 29 (14%) 63 (46%) 41 (57%) 28 (26%) 38 (45%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
e_l_s




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 1 (1.2%)
s_l_b




    FALSE 29 (14%) 63 (46%) 42 (58%) 36 (34%) 39 (46%)
    TRUE 172 (86%) 74 (54%) 30 (42%) 71 (66%) 46 (54%)
s_l_e




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 84 (99%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 0 (0%) 0 (0%) 1 (0.9%) 1 (1.2%)
    TRUE 200 (100%) 137 (100%) 72 (100%) 106 (99%) 84 (99%)
b_l_s




    FALSE 149 (74%) 76 (55%) 34 (47%) 73 (68%) 46 (54%)
    TRUE 52 (26%) 61 (45%) 38 (53%) 34 (32%) 39 (46%)
e_l_b




    FALSE 200 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 1 (0.5%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
e_l_s




    FALSE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 1 (1.2%)
s_l_b




    FALSE 58 (29%) 62 (45%) 39 (54%) 37 (35%) 40 (47%)
    TRUE 143 (71%) 75 (55%) 33 (46%) 70 (65%) 45 (53%)
s_l_e




    FALSE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 84 (99%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 8

chrom <- 8
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 175 (87%) 105 (77%) 63 (88%) 90 (84%) 63 (74%)
    TRUE 26 (13%) 32 (23%) 9 (13%) 17 (16%) 22 (26%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 31 (15%) 35 (26%) 10 (14%) 23 (21%) 25 (29%)
    TRUE 170 (85%) 102 (74%) 62 (86%) 84 (79%) 60 (71%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 2 (1.0%) 1 (0.7%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 199 (99%) 136 (99%) 72 (100%) 106 (99%) 85 (100%)
b_l_s




    FALSE 131 (65%) 53 (39%) 29 (40%) 59 (55%) 46 (54%)
    TRUE 70 (35%) 84 (61%) 43 (60%) 48 (45%) 39 (46%)
e_l_b




    FALSE 199 (99%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 2 (1.0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
e_l_s




    FALSE 199 (99%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 2 (1.0%) 0 (0%) 0 (0%) 0 (0%) 0 (0%)
s_l_b




    FALSE 76 (38%) 87 (64%) 45 (63%) 50 (47%) 43 (51%)
    TRUE 125 (62%) 50 (36%) 27 (38%) 57 (53%) 42 (49%)
s_l_e




    FALSE 2 (1.0%) 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 199 (99%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 9

chrom <- 9
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 0 (0%) 3 (2.2%) 0 (0%) 2 (1.9%) 1 (1.2%)
    TRUE 201 (100%) 134 (98%) 72 (100%) 105 (98%) 84 (99%)
b_l_s




    FALSE 165 (82%) 92 (67%) 42 (58%) 79 (74%) 58 (68%)
    TRUE 36 (18%) 45 (33%) 30 (42%) 28 (26%) 27 (32%)
e_l_b




    FALSE 201 (100%) 135 (99%) 72 (100%) 105 (98%) 84 (99%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 2 (1.9%) 1 (1.2%)
e_l_s




    FALSE 199 (99%) 136 (99%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 2 (1.0%) 1 (0.7%) 0 (0%) 0 (0%) 1 (1.2%)
s_l_b




    FALSE 38 (19%) 45 (33%) 31 (43%) 31 (29%) 32 (38%)
    TRUE 163 (81%) 92 (67%) 41 (57%) 76 (71%) 53 (62%)
s_l_e




    FALSE 2 (1.0%) 1 (0.7%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 199 (99%) 136 (99%) 72 (100%) 107 (100%) 84 (99%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 2 (1.0%) 0 (0%) 0 (0%) 4 (3.7%) 2 (2.4%)
    TRUE 199 (99%) 137 (100%) 72 (100%) 103 (96%) 83 (98%)
b_l_s




    FALSE 151 (75%) 72 (53%) 39 (54%) 73 (68%) 50 (59%)
    TRUE 50 (25%) 65 (47%) 33 (46%) 34 (32%) 35 (41%)
e_l_b




    FALSE 200 (100%) 137 (100%) 72 (100%) 104 (97%) 84 (99%)
    TRUE 1 (0.5%) 0 (0%) 0 (0%) 3 (2.8%) 1 (1.2%)
e_l_s




    FALSE 200 (100%) 135 (99%) 72 (100%) 106 (99%) 83 (98%)
    TRUE 1 (0.5%) 2 (1.5%) 0 (0%) 1 (0.9%) 2 (2.4%)
s_l_b




    FALSE 56 (28%) 68 (50%) 36 (50%) 39 (36%) 36 (42%)
    TRUE 145 (72%) 69 (50%) 36 (50%) 68 (64%) 49 (58%)
s_l_e




    FALSE 1 (0.5%) 2 (1.5%) 0 (0%) 1 (0.9%) 2 (2.4%)
    TRUE 200 (100%) 135 (99%) 72 (100%) 106 (99%) 83 (98%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 10

chrom <- 10
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 152 (76%) 79 (58%) 37 (51%) 79 (74%) 51 (60%)
    TRUE 49 (24%) 58 (42%) 35 (49%) 28 (26%) 34 (40%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 53 (26%) 59 (43%) 35 (49%) 30 (28%) 37 (44%)
    TRUE 148 (74%) 78 (57%) 37 (51%) 77 (72%) 48 (56%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 153 (76%) 84 (61%) 33 (46%) 78 (73%) 47 (55%)
    TRUE 48 (24%) 53 (39%) 39 (54%) 29 (27%) 38 (45%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 53 (26%) 58 (42%) 40 (56%) 32 (30%) 40 (47%)
    TRUE 148 (74%) 79 (58%) 32 (44%) 75 (70%) 45 (53%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 11

chrom <- 11
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 144 (72%) 78 (57%) 39 (54%) 68 (64%) 50 (59%)
    TRUE 57 (28%) 59 (43%) 33 (46%) 39 (36%) 35 (41%)
e_l_b




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 62 (31%) 61 (45%) 35 (49%) 44 (41%) 36 (42%)
    TRUE 139 (69%) 76 (55%) 37 (51%) 63 (59%) 49 (58%)
s_l_e




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 3 (1.5%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 198 (99%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 131 (65%) 68 (50%) 37 (51%) 69 (64%) 52 (61%)
    TRUE 70 (35%) 69 (50%) 35 (49%) 38 (36%) 33 (39%)
e_l_b




    FALSE 198 (99%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 3 (1.5%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
e_l_s




    FALSE 200 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 1 (0.5%) 0 (0%) 0 (0%) 0 (0%) 0 (0%)
s_l_b




    FALSE 75 (37%) 74 (54%) 37 (51%) 39 (36%) 37 (44%)
    TRUE 126 (63%) 63 (46%) 35 (49%) 68 (64%) 48 (56%)
s_l_e




    FALSE 1 (0.5%) 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 200 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 12

chrom <- 12
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 200 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
b_l_s




    FALSE 147 (73%) 79 (58%) 35 (49%) 71 (66%) 44 (52%)
    TRUE 54 (27%) 58 (42%) 37 (51%) 36 (34%) 41 (48%)
e_l_b




    FALSE 200 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 1 (0.5%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
s_l_b




    FALSE 58 (29%) 61 (45%) 39 (54%) 40 (37%) 43 (51%)
    TRUE 143 (71%) 76 (55%) 33 (46%) 67 (63%) 42 (49%)
s_l_e




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 84 (99%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
b_l_s




    FALSE 143 (71%) 69 (50%) 33 (46%) 65 (61%) 45 (53%)
    TRUE 58 (29%) 68 (50%) 39 (54%) 42 (39%) 40 (47%)
e_l_b




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
e_l_s




    FALSE 200 (100%) 137 (100%) 72 (100%) 106 (99%) 84 (99%)
    TRUE 1 (0.5%) 0 (0%) 0 (0%) 1 (0.9%) 1 (1.2%)
s_l_b




    FALSE 61 (30%) 72 (53%) 42 (58%) 45 (42%) 42 (49%)
    TRUE 140 (70%) 65 (47%) 30 (42%) 62 (58%) 43 (51%)
s_l_e




    FALSE 1 (0.5%) 2 (1.5%) 0 (0%) 1 (0.9%) 1 (1.2%)
    TRUE 200 (100%) 135 (99%) 72 (100%) 106 (99%) 84 (99%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 13

chrom <- 13
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 1 (0.7%) 1 (1.4%) 2 (1.9%) 1 (1.2%)
    TRUE 200 (100%) 136 (99%) 71 (99%) 105 (98%) 84 (99%)
b_l_s




    FALSE 148 (74%) 80 (58%) 41 (57%) 68 (64%) 50 (59%)
    TRUE 53 (26%) 57 (42%) 31 (43%) 39 (36%) 35 (41%)
e_l_b




    FALSE 201 (100%) 136 (99%) 71 (99%) 105 (98%) 84 (99%)
    TRUE 0 (0%) 1 (0.7%) 1 (1.4%) 2 (1.9%) 1 (1.2%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
s_l_b




    FALSE 62 (31%) 63 (46%) 31 (43%) 40 (37%) 39 (46%)
    TRUE 139 (69%) 74 (54%) 41 (57%) 67 (63%) 46 (54%)
s_l_e




    FALSE 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (1.2%)
    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 84 (99%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 1 (0.7%) 0 (0%) 2 (1.9%) 1 (1.2%)
    TRUE 200 (100%) 136 (99%) 72 (100%) 105 (98%) 84 (99%)
b_l_s




    FALSE 128 (64%) 61 (45%) 35 (49%) 65 (61%) 42 (49%)
    TRUE 73 (36%) 76 (55%) 37 (51%) 42 (39%) 43 (51%)
e_l_b




    FALSE 200 (100%) 136 (99%) 72 (100%) 105 (98%) 84 (99%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 2 (1.9%) 1 (1.2%)
e_l_s




    FALSE 200 (100%) 135 (99%) 72 (100%) 105 (98%) 85 (100%)
    TRUE 1 (0.5%) 2 (1.5%) 0 (0%) 2 (1.9%) 0 (0%)
s_l_b




    FALSE 81 (40%) 82 (60%) 39 (54%) 45 (42%) 48 (56%)
    TRUE 120 (60%) 55 (40%) 33 (46%) 62 (58%) 37 (44%)
s_l_e




    FALSE 1 (0.5%) 2 (1.5%) 0 (0%) 2 (1.9%) 0 (0%)
    TRUE 200 (100%) 135 (99%) 72 (100%) 105 (98%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 14

chrom <- 14
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 200 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 146 (73%) 67 (49%) 38 (53%) 65 (61%) 45 (53%)
    TRUE 55 (27%) 70 (51%) 34 (47%) 42 (39%) 40 (47%)
e_l_b




    FALSE 200 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
e_l_s




    FALSE 200 (100%) 135 (99%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 1 (0.5%) 2 (1.5%) 0 (0%) 1 (0.9%) 0 (0%)
s_l_b




    FALSE 61 (30%) 75 (55%) 37 (51%) 46 (43%) 41 (48%)
    TRUE 140 (70%) 62 (45%) 35 (49%) 61 (57%) 44 (52%)
s_l_e




    FALSE 1 (0.5%) 2 (1.5%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 200 (100%) 135 (99%) 72 (100%) 106 (99%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 2 (1.0%) 1 (0.7%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 199 (99%) 136 (99%) 72 (100%) 106 (99%) 85 (100%)
b_l_s




    FALSE 127 (63%) 68 (50%) 37 (51%) 64 (60%) 41 (48%)
    TRUE 74 (37%) 69 (50%) 35 (49%) 43 (40%) 44 (52%)
e_l_b




    FALSE 199 (99%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 2 (1.0%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
e_l_s




    FALSE 200 (100%) 137 (100%) 71 (99%) 106 (99%) 84 (99%)
    TRUE 1 (0.5%) 0 (0%) 1 (1.4%) 1 (0.9%) 1 (1.2%)
s_l_b




    FALSE 80 (40%) 74 (54%) 41 (57%) 45 (42%) 46 (54%)
    TRUE 121 (60%) 63 (46%) 31 (43%) 62 (58%) 39 (46%)
s_l_e




    FALSE 3 (1.5%) 0 (0%) 1 (1.4%) 1 (0.9%) 2 (2.4%)
    TRUE 198 (99%) 137 (100%) 71 (99%) 106 (99%) 83 (98%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 15

chrom <- 15
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 6 (3.0%) 2 (1.5%) 0 (0%) 2 (1.9%) 1 (1.2%)
    TRUE 195 (97%) 135 (99%) 72 (100%) 105 (98%) 84 (99%)
b_l_s




    FALSE 138 (69%) 77 (56%) 41 (57%) 74 (69%) 53 (62%)
    TRUE 63 (31%) 60 (44%) 31 (43%) 33 (31%) 32 (38%)
e_l_b




    FALSE 196 (98%) 136 (99%) 72 (100%) 105 (98%) 84 (99%)
    TRUE 5 (2.5%) 1 (0.7%) 0 (0%) 2 (1.9%) 1 (1.2%)
e_l_s




    FALSE 199 (99%) 133 (97%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 2 (1.0%) 4 (2.9%) 0 (0%) 0 (0%) 0 (0%)
s_l_b




    FALSE 64 (32%) 64 (47%) 31 (43%) 39 (36%) 36 (42%)
    TRUE 137 (68%) 73 (53%) 41 (57%) 68 (64%) 49 (58%)
s_l_e




    FALSE 2 (1.0%) 4 (2.9%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 199 (99%) 133 (97%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 4 (2.0%) 2 (1.5%) 1 (1.4%) 2 (1.9%) 0 (0%)
    TRUE 197 (98%) 135 (99%) 71 (99%) 105 (98%) 85 (100%)
b_l_s




    FALSE 138 (69%) 69 (50%) 34 (47%) 70 (65%) 37 (44%)
    TRUE 63 (31%) 68 (50%) 38 (53%) 37 (35%) 48 (56%)
e_l_b




    FALSE 197 (98%) 135 (99%) 71 (99%) 106 (99%) 85 (100%)
    TRUE 4 (2.0%) 2 (1.5%) 1 (1.4%) 1 (0.9%) 0 (0%)
e_l_s




    FALSE 200 (100%) 136 (99%) 72 (100%) 106 (99%) 83 (98%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 1 (0.9%) 2 (2.4%)
s_l_b




    FALSE 68 (34%) 73 (53%) 38 (53%) 42 (39%) 51 (60%)
    TRUE 133 (66%) 64 (47%) 34 (47%) 65 (61%) 34 (40%)
s_l_e




    FALSE 1 (0.5%) 1 (0.7%) 1 (1.4%) 1 (0.9%) 2 (2.4%)
    TRUE 200 (100%) 136 (99%) 71 (99%) 106 (99%) 83 (98%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 16

chrom <- 16
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 1 (0.7%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 200 (100%) 136 (99%) 72 (100%) 106 (99%) 85 (100%)
b_l_s




    FALSE 150 (75%) 76 (55%) 47 (65%) 70 (65%) 51 (60%)
    TRUE 51 (25%) 61 (45%) 25 (35%) 37 (35%) 34 (40%)
e_l_b




    FALSE 200 (100%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 1 (0.5%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
e_l_s




    FALSE 201 (100%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
s_l_b




    FALSE 55 (27%) 62 (45%) 27 (38%) 41 (38%) 39 (46%)
    TRUE 146 (73%) 75 (55%) 45 (63%) 66 (62%) 46 (54%)
s_l_e




    FALSE 0 (0%) 0 (0%) 0 (0%) 2 (1.9%) 0 (0%)
    TRUE 201 (100%) 137 (100%) 72 (100%) 105 (98%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 0 (0%) 1 (1.4%) 0 (0%) 3 (3.5%)
    TRUE 200 (100%) 137 (100%) 71 (99%) 107 (100%) 82 (96%)
b_l_s




    FALSE 146 (73%) 67 (49%) 27 (38%) 51 (48%) 39 (46%)
    TRUE 55 (27%) 70 (51%) 45 (63%) 56 (52%) 46 (54%)
e_l_b




    FALSE 200 (100%) 137 (100%) 71 (99%) 107 (100%) 82 (96%)
    TRUE 1 (0.5%) 0 (0%) 1 (1.4%) 0 (0%) 3 (3.5%)
e_l_s




    FALSE 200 (100%) 135 (99%) 72 (100%) 107 (100%) 80 (94%)
    TRUE 1 (0.5%) 2 (1.5%) 0 (0%) 0 (0%) 5 (5.9%)
s_l_b




    FALSE 59 (29%) 74 (54%) 46 (64%) 57 (53%) 47 (55%)
    TRUE 142 (71%) 63 (46%) 26 (36%) 50 (47%) 38 (45%)
s_l_e




    FALSE 1 (0.5%) 3 (2.2%) 0 (0%) 0 (0%) 6 (7.1%)
    TRUE 200 (100%) 134 (98%) 72 (100%) 107 (100%) 79 (93%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 17

chrom <- 17
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 0 (0%) 4 (2.9%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 133 (97%) 72 (100%) 106 (99%) 85 (100%)
b_l_s




    FALSE 156 (78%) 99 (72%) 41 (57%) 77 (72%) 52 (61%)
    TRUE 45 (22%) 38 (28%) 31 (43%) 30 (28%) 33 (39%)
e_l_b




    FALSE 201 (100%) 134 (98%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 1 (0.9%) 0 (0%)
e_l_s




    FALSE 200 (100%) 136 (99%) 71 (99%) 107 (100%) 85 (100%)
    TRUE 1 (0.5%) 1 (0.7%) 1 (1.4%) 0 (0%) 0 (0%)
s_l_b




    FALSE 48 (24%) 44 (32%) 34 (47%) 36 (34%) 35 (41%)
    TRUE 153 (76%) 93 (68%) 38 (53%) 71 (66%) 50 (59%)
s_l_e




    FALSE 1 (0.5%) 1 (0.7%) 1 (1.4%) 0 (0%) 0 (0%)
    TRUE 200 (100%) 136 (99%) 71 (99%) 107 (100%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 1 (0.5%) 1 (0.7%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 200 (100%) 136 (99%) 72 (100%) 106 (99%) 85 (100%)
b_l_s




    FALSE 133 (66%) 85 (62%) 32 (44%) 67 (63%) 56 (66%)
    TRUE 68 (34%) 52 (38%) 40 (56%) 40 (37%) 29 (34%)
e_l_b




    FALSE 201 (100%) 136 (99%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 1 (0.9%) 0 (0%)
e_l_s




    FALSE 199 (99%) 136 (99%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 2 (1.0%) 1 (0.7%) 0 (0%) 1 (0.9%) 0 (0%)
s_l_b




    FALSE 71 (35%) 61 (45%) 43 (60%) 43 (40%) 31 (36%)
    TRUE 130 (65%) 76 (55%) 29 (40%) 64 (60%) 54 (64%)
s_l_e




    FALSE 2 (1.0%) 1 (0.7%) 0 (0%) 1 (0.9%) 1 (1.2%)
    TRUE 199 (99%) 136 (99%) 72 (100%) 106 (99%) 84 (99%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 18

chrom <- 18
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 2 (1.0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 199 (99%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
b_l_s




    FALSE 139 (69%) 74 (54%) 37 (51%) 60 (56%) 50 (59%)
    TRUE 62 (31%) 63 (46%) 35 (49%) 47 (44%) 35 (41%)
e_l_b




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
e_l_s




    FALSE 200 (100%) 136 (99%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 1 (0.5%) 1 (0.7%) 0 (0%) 1 (0.9%) 0 (0%)
s_l_b




    FALSE 65 (32%) 66 (48%) 40 (56%) 53 (50%) 38 (45%)
    TRUE 136 (68%) 71 (52%) 32 (44%) 54 (50%) 47 (55%)
s_l_e




    FALSE 1 (0.5%) 2 (1.5%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 200 (100%) 135 (99%) 72 (100%) 106 (99%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 4 (2.0%) 5 (3.6%) 0 (0%) 3 (2.8%) 1 (1.2%)
    TRUE 197 (98%) 132 (96%) 72 (100%) 104 (97%) 84 (99%)
b_l_s




    FALSE 130 (65%) 72 (53%) 36 (50%) 56 (52%) 50 (59%)
    TRUE 71 (35%) 65 (47%) 36 (50%) 51 (48%) 35 (41%)
e_l_b




    FALSE 197 (98%) 134 (98%) 72 (100%) 104 (97%) 84 (99%)
    TRUE 4 (2.0%) 3 (2.2%) 0 (0%) 3 (2.8%) 1 (1.2%)
e_l_s




    FALSE 200 (100%) 130 (95%) 70 (97%) 106 (99%) 85 (100%)
    TRUE 1 (0.5%) 7 (5.1%) 2 (2.8%) 1 (0.9%) 0 (0%)
s_l_b




    FALSE 79 (39%) 70 (51%) 37 (51%) 57 (53%) 38 (45%)
    TRUE 122 (61%) 67 (49%) 35 (49%) 50 (47%) 47 (55%)
s_l_e




    FALSE 1 (0.5%) 7 (5.1%) 2 (2.8%) 2 (1.9%) 0 (0%)
    TRUE 200 (100%) 130 (95%) 70 (97%) 105 (98%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 19

chrom <- 19
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 2 (1.0%) 1 (0.7%) 1 (1.4%) 0 (0%) 4 (4.7%)
    TRUE 199 (99%) 136 (99%) 71 (99%) 107 (100%) 81 (95%)
b_l_s




    FALSE 153 (76%) 89 (65%) 40 (56%) 60 (56%) 60 (71%)
    TRUE 48 (24%) 48 (35%) 32 (44%) 47 (44%) 25 (29%)
e_l_b




    FALSE 199 (99%) 136 (99%) 72 (100%) 107 (100%) 82 (96%)
    TRUE 2 (1.0%) 1 (0.7%) 0 (0%) 0 (0%) 3 (3.5%)
e_l_s




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 82 (96%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 3 (3.5%)
s_l_b




    FALSE 55 (27%) 51 (37%) 32 (44%) 50 (47%) 28 (33%)
    TRUE 146 (73%) 86 (63%) 40 (56%) 57 (53%) 57 (67%)
s_l_e




    FALSE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 3 (3.5%)
    TRUE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 82 (96%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 4 (2.0%) 8 (5.8%) 1 (1.4%) 3 (2.8%) 0 (0%)
    TRUE 197 (98%) 129 (94%) 71 (99%) 104 (97%) 85 (100%)
b_l_s




    FALSE 139 (69%) 83 (61%) 37 (51%) 67 (63%) 47 (55%)
    TRUE 62 (31%) 54 (39%) 35 (49%) 40 (37%) 38 (45%)
e_l_b




    FALSE 197 (98%) 130 (95%) 72 (100%) 104 (97%) 85 (100%)
    TRUE 4 (2.0%) 7 (5.1%) 0 (0%) 3 (2.8%) 0 (0%)
e_l_s




    FALSE 201 (100%) 132 (96%) 70 (97%) 107 (100%) 80 (94%)
    TRUE 0 (0%) 5 (3.6%) 2 (2.8%) 0 (0%) 5 (5.9%)
s_l_b




    FALSE 70 (35%) 57 (42%) 37 (51%) 46 (43%) 38 (45%)
    TRUE 131 (65%) 80 (58%) 35 (49%) 61 (57%) 47 (55%)
s_l_e




    FALSE 0 (0%) 5 (3.6%) 2 (2.8%) 1 (0.9%) 6 (7.1%)
    TRUE 201 (100%) 132 (96%) 70 (97%) 106 (99%) 79 (93%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 20

chrom <- 20
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 3 (1.5%) 2 (1.5%) 2 (2.8%) 3 (2.8%) 0 (0%)
    TRUE 198 (99%) 135 (99%) 70 (97%) 104 (97%) 85 (100%)
b_l_s




    FALSE 164 (82%) 78 (57%) 44 (61%) 76 (71%) 54 (64%)
    TRUE 37 (18%) 59 (43%) 28 (39%) 31 (29%) 31 (36%)
e_l_b




    FALSE 199 (99%) 137 (100%) 70 (97%) 104 (97%) 85 (100%)
    TRUE 2 (1.0%) 0 (0%) 2 (2.8%) 3 (2.8%) 0 (0%)
e_l_s




    FALSE 201 (100%) 134 (98%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 1 (0.9%) 0 (0%)
s_l_b




    FALSE 40 (20%) 63 (46%) 31 (43%) 35 (33%) 34 (40%)
    TRUE 161 (80%) 74 (54%) 41 (57%) 72 (67%) 51 (60%)
s_l_e




    FALSE 0 (0%) 3 (2.2%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 134 (98%) 72 (100%) 106 (99%) 85 (100%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 4 (2.0%) 5 (3.6%) 2 (2.8%) 4 (3.7%) 0 (0%)
    TRUE 197 (98%) 132 (96%) 70 (97%) 103 (96%) 85 (100%)
b_l_s




    FALSE 145 (72%) 77 (56%) 40 (56%) 67 (63%) 52 (61%)
    TRUE 56 (28%) 60 (44%) 32 (44%) 40 (37%) 33 (39%)
e_l_b




    FALSE 199 (99%) 134 (98%) 70 (97%) 103 (96%) 85 (100%)
    TRUE 2 (1.0%) 3 (2.2%) 2 (2.8%) 4 (3.7%) 0 (0%)
e_l_s




    FALSE 200 (100%) 135 (99%) 71 (99%) 107 (100%) 84 (99%)
    TRUE 1 (0.5%) 2 (1.5%) 1 (1.4%) 0 (0%) 1 (1.2%)
s_l_b




    FALSE 59 (29%) 63 (46%) 32 (44%) 42 (39%) 34 (40%)
    TRUE 142 (71%) 74 (54%) 40 (56%) 65 (61%) 51 (60%)
s_l_e




    FALSE 1 (0.5%) 2 (1.5%) 1 (1.4%) 0 (0%) 1 (1.2%)
    TRUE 200 (100%) 135 (99%) 71 (99%) 107 (100%) 84 (99%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 21

chrom <- 21
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 7 (3.5%) 12 (8.8%) 6 (8.3%) 14 (13%) 6 (7.1%)
    TRUE 194 (97%) 125 (91%) 66 (92%) 93 (87%) 79 (93%)
b_l_s




    FALSE 125 (62%) 69 (50%) 39 (54%) 67 (63%) 48 (56%)
    TRUE 76 (38%) 68 (50%) 33 (46%) 40 (37%) 37 (44%)
e_l_b




    FALSE 196 (98%) 127 (93%) 67 (93%) 98 (92%) 81 (95%)
    TRUE 5 (2.5%) 10 (7.3%) 5 (6.9%) 9 (8.4%) 4 (4.7%)
e_l_s




    FALSE 197 (98%) 123 (90%) 69 (96%) 99 (93%) 84 (99%)
    TRUE 4 (2.0%) 14 (10%) 3 (4.2%) 8 (7.5%) 1 (1.2%)
s_l_b




    FALSE 80 (40%) 73 (53%) 35 (49%) 45 (42%) 37 (44%)
    TRUE 121 (60%) 64 (47%) 37 (51%) 62 (58%) 48 (56%)
s_l_e




    FALSE 5 (2.5%) 15 (11%) 3 (4.2%) 10 (9.3%) 2 (2.4%)
    TRUE 196 (98%) 122 (89%) 69 (96%) 97 (91%) 83 (98%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 13 (6.5%) 15 (11%) 5 (6.9%) 18 (17%) 5 (5.9%)
    TRUE 188 (94%) 122 (89%) 67 (93%) 89 (83%) 80 (94%)
b_l_s




    FALSE 122 (61%) 69 (50%) 40 (56%) 56 (52%) 37 (44%)
    TRUE 79 (39%) 68 (50%) 32 (44%) 51 (48%) 48 (56%)
e_l_b




    FALSE 192 (96%) 125 (91%) 68 (94%) 89 (83%) 80 (94%)
    TRUE 9 (4.5%) 12 (8.8%) 4 (5.6%) 18 (17%) 5 (5.9%)
e_l_s




    FALSE 191 (95%) 119 (87%) 69 (96%) 101 (94%) 82 (96%)
    TRUE 10 (5.0%) 18 (13%) 3 (4.2%) 6 (5.6%) 3 (3.5%)
s_l_b




    FALSE 91 (45%) 77 (56%) 36 (50%) 54 (50%) 51 (60%)
    TRUE 110 (55%) 60 (44%) 36 (50%) 53 (50%) 34 (40%)
s_l_e




    FALSE 14 (7.0%) 20 (15%) 3 (4.2%) 9 (8.4%) 3 (3.5%)
    TRUE 187 (93%) 117 (85%) 69 (96%) 98 (92%) 82 (96%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_switches(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 9 (4.5%) 5 (3.6%) 3 (4.2%) 6 (5.6%) 4 (4.7%)
    TRUE 192 (96%) 132 (96%) 69 (96%) 101 (94%) 81 (95%)
b_l_s




    FALSE 153 (76%) 82 (60%) 42 (58%) 73 (68%) 57 (67%)
    TRUE 48 (24%) 55 (40%) 30 (42%) 34 (32%) 28 (33%)
e_l_b




    FALSE 195 (97%) 132 (96%) 70 (97%) 101 (94%) 81 (95%)
    TRUE 6 (3.0%) 5 (3.6%) 2 (2.8%) 6 (5.6%) 4 (4.7%)
e_l_s




    FALSE 198 (99%) 133 (97%) 70 (97%) 106 (99%) 83 (98%)
    TRUE 3 (1.5%) 4 (2.9%) 2 (2.8%) 1 (0.9%) 2 (2.4%)
s_l_b




    FALSE 57 (28%) 59 (43%) 32 (44%) 36 (34%) 30 (35%)
    TRUE 144 (72%) 78 (57%) 40 (56%) 71 (66%) 55 (65%)
s_l_e




    FALSE 4 (2.0%) 5 (3.6%) 2 (2.8%) 3 (2.8%) 3 (3.5%)
    TRUE 197 (98%) 132 (96%) 70 (97%) 104 (97%) 82 (96%)
1 n (%)
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 10 (5.0%) 13 (9.5%) 4 (5.6%) 16 (15%) 10 (12%)
    TRUE 191 (95%) 124 (91%) 68 (94%) 91 (85%) 75 (88%)
b_l_s




    FALSE 149 (74%) 79 (58%) 41 (57%) 57 (53%) 53 (62%)
    TRUE 52 (26%) 58 (42%) 31 (43%) 50 (47%) 32 (38%)
e_l_b




    FALSE 195 (97%) 126 (92%) 68 (94%) 94 (88%) 76 (89%)
    TRUE 6 (3.0%) 11 (8.0%) 4 (5.6%) 13 (12%) 9 (11%)
e_l_s




    FALSE 198 (99%) 130 (95%) 68 (94%) 94 (88%) 76 (89%)
    TRUE 3 (1.5%) 7 (5.1%) 4 (5.6%) 13 (12%) 9 (11%)
s_l_b




    FALSE 56 (28%) 65 (47%) 34 (47%) 54 (50%) 33 (39%)
    TRUE 145 (72%) 72 (53%) 38 (53%) 53 (50%) 52 (61%)
s_l_e




    FALSE 3 (1.5%) 7 (5.1%) 4 (5.6%) 14 (13%) 9 (11%)
    TRUE 198 (99%) 130 (95%) 68 (94%) 93 (87%) 76 (89%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Chromosome X

plot_switches(df_switch_x, "Beagle", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switches(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
table_switches(df_switch_x, "pop")
Characteristic AFR
N = 200
1
AMR
N = 200
1
EAS
N = 200
1
EUR
N = 200
1
SAS
N = 200
1
b_l_e




    FALSE 0 (0%) 0 (0%) 1 (0.5%) 0 (0%) 0 (0%)
    TRUE 200 (100%) 200 (100%) 199 (100%) 200 (100%) 200 (100%)
b_l_s




    FALSE 174 (87%) 150 (75%) 163 (82%) 162 (81%) 166 (83%)
    TRUE 26 (13%) 50 (25%) 37 (19%) 38 (19%) 34 (17%)
e_l_b




    FALSE 200 (100%) 200 (100%) 199 (100%) 200 (100%) 200 (100%)
    TRUE 0 (0%) 0 (0%) 1 (0.5%) 0 (0%) 0 (0%)
e_l_s




    FALSE 200 (100%) 200 (100%) 200 (100%) 200 (100%) 200 (100%)
s_l_b




    FALSE 30 (15%) 58 (29%) 45 (23%) 49 (25%) 39 (20%)
    TRUE 170 (85%) 142 (71%) 155 (78%) 151 (76%) 161 (81%)
s_l_e




    TRUE 200 (100%) 200 (100%) 200 (100%) 200 (100%) 200 (100%)
1 n (%)
cross_meth_plot(df_switch_x, "Switches", plot_switches, "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19

Switch Rate

plot_switch_rate <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_other_beagle / n_hets,
         Eagle = n_other_eagle / n_hets,
         SHAPEIT = n_other_shapeit / n_hets) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switch Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_switch_rate_noth <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_switch_b / n_het,
         Eagle = n_switch_e / n_het,
         SHAPEIT = n_switch_s / n_het) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switch Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

Chromosome 1

chrom <- 1
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 2

chrom <- 2
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 3

chrom <- 3
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 4

chrom <- 4
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 5

chrom <- 5
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 6

chrom <- 6
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 7

chrom <- 7
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 8

chrom <- 8
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 9

chrom <- 9
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 10

chrom <- 10
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 11

chrom <- 11
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 12

chrom <- 12
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 13

chrom <- 13
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 14

chrom <- 14
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 15

chrom <- 15
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 16

chrom <- 16
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 17

chrom <- 17
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 18

chrom <- 18
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 19

chrom <- 19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 20

chrom <- 20
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 21

chrom <- 21
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Chromosome X

plot_switch_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_switch_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
cross_meth_plot(df_switch_x, "Switches", plot_switch_rate, "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19

Flips

plot_flips <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_beagle,
         Eagle = n_flip_eagle,
         SHAPEIT = n_flip_shapeit) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Flips", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_flips_noth <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_b,
         Eagle = n_flip_e,
         SHAPEIT = n_flip_s) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Flips", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

table_flip <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_flip_beagle ),
         Eagle =  (n_flip_eagle),
         SHAPEIT =  (n_flip_shapeit)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

table_flip_noth <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_flip_b ),
         Eagle =  (n_flip_e),
         SHAPEIT =  (n_flip_s)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

Chromosome 1

chrom <- 1
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 134 (98%) 69 (96%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 3 (4.2%) 0 (0%) 0 (0%)
b_l_s




    FALSE 2 (1.0%) 2 (1.5%) 2 (2.8%) 0 (0%) 0 (0%)
    TRUE 199 (99%) 135 (99%) 70 (97%) 107 (100%) 85 (100%)
e_l_b




    FALSE 0 (0%) 3 (2.2%) 3 (4.2%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 134 (98%) 69 (96%) 107 (100%) 85 (100%)
e_l_s




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 199 (99%) 135 (99%) 70 (97%) 107 (100%) 85 (100%)
    TRUE 2 (1.0%) 2 (1.5%) 2 (2.8%) 0 (0%) 0 (0%)
s_l_e




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 131 (96%) 70 (97%) 102 (95%) 85 (100%)
    TRUE 0 (0%) 6 (4.4%) 2 (2.8%) 5 (4.7%) 0 (0%)
b_l_s




    FALSE 2 (1.0%) 9 (6.6%) 4 (5.6%) 10 (9.3%) 1 (1.2%)
    TRUE 199 (99%) 128 (93%) 68 (94%) 97 (91%) 84 (99%)
e_l_b




    FALSE 0 (0%) 6 (4.4%) 2 (2.8%) 5 (4.7%) 0 (0%)
    TRUE 201 (100%) 131 (96%) 70 (97%) 102 (95%) 85 (100%)
e_l_s




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 199 (99%) 129 (94%) 68 (94%) 97 (91%) 85 (100%)
    TRUE 2 (1.0%) 8 (5.8%) 4 (5.6%) 10 (9.3%) 0 (0%)
s_l_e




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 2

chrom <- 2
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 128 (93%) 70 (97%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 9 (6.6%) 2 (2.8%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 3 (1.5%) 7 (5.1%) 2 (2.8%) 8 (7.5%) 1 (1.2%)
    TRUE 198 (99%) 130 (95%) 70 (97%) 99 (93%) 84 (99%)
e_l_b




    FALSE 0 (0%) 9 (6.6%) 2 (2.8%) 2 (1.9%) 0 (0%)
    TRUE 201 (100%) 128 (93%) 70 (97%) 105 (98%) 85 (100%)
e_l_s




    FALSE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 199 (99%) 132 (96%) 70 (97%) 100 (93%) 84 (99%)
    TRUE 2 (1.0%) 5 (3.6%) 2 (2.8%) 7 (6.5%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 134 (98%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 1 (0.9%) 0 (0%)
b_l_s




    FALSE 4 (2.0%) 5 (3.6%) 1 (1.4%) 2 (1.9%) 0 (0%)
    TRUE 197 (98%) 132 (96%) 71 (99%) 105 (98%) 85 (100%)
e_l_b




    FALSE 0 (0%) 4 (2.9%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 133 (97%) 72 (100%) 106 (99%) 85 (100%)
e_l_s




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 197 (98%) 132 (96%) 71 (99%) 105 (98%) 85 (100%)
    TRUE 4 (2.0%) 5 (3.6%) 1 (1.4%) 2 (1.9%) 0 (0%)
s_l_e




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 3

chrom <- 3
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 131 (96%) 70 (97%) 104 (97%) 85 (100%)
    TRUE 0 (0%) 6 (4.4%) 2 (2.8%) 3 (2.8%) 0 (0%)
b_l_s




    FALSE 3 (1.5%) 7 (5.1%) 4 (5.6%) 4 (3.7%) 1 (1.2%)
    TRUE 198 (99%) 130 (95%) 68 (94%) 103 (96%) 84 (99%)
e_l_b




    FALSE 0 (0%) 7 (5.1%) 2 (2.8%) 3 (2.8%) 0 (0%)
    TRUE 201 (100%) 130 (95%) 70 (97%) 104 (97%) 85 (100%)
e_l_s




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 198 (99%) 130 (95%) 69 (96%) 104 (97%) 84 (99%)
    TRUE 3 (1.5%) 7 (5.1%) 3 (4.2%) 3 (2.8%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 200 (100%) 134 (98%) 71 (99%) 100 (93%) 84 (99%)
    TRUE 1 (0.5%) 3 (2.2%) 1 (1.4%) 7 (6.5%) 1 (1.2%)
b_l_s




    FALSE 4 (2.0%) 8 (5.8%) 6 (8.3%) 7 (6.5%) 1 (1.2%)
    TRUE 197 (98%) 129 (94%) 66 (92%) 100 (93%) 84 (99%)
e_l_b




    FALSE 1 (0.5%) 3 (2.2%) 1 (1.4%) 7 (6.5%) 1 (1.2%)
    TRUE 200 (100%) 134 (98%) 71 (99%) 100 (93%) 84 (99%)
e_l_s




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 197 (98%) 129 (94%) 67 (93%) 101 (94%) 84 (99%)
    TRUE 4 (2.0%) 8 (5.8%) 5 (6.9%) 6 (5.6%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 4

chrom <- 4
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 133 (97%) 71 (99%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 4 (2.9%) 1 (1.4%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 8 (4.0%) 7 (5.1%) 1 (1.4%) 5 (4.7%) 0 (0%)
    TRUE 193 (96%) 130 (95%) 71 (99%) 102 (95%) 85 (100%)
e_l_b




    FALSE 0 (0%) 5 (3.6%) 1 (1.4%) 3 (2.8%) 0 (0%)
    TRUE 201 (100%) 132 (96%) 71 (99%) 104 (97%) 85 (100%)
e_l_s




    FALSE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 193 (96%) 130 (95%) 71 (99%) 102 (95%) 85 (100%)
    TRUE 8 (4.0%) 7 (5.1%) 1 (1.4%) 5 (4.7%) 0 (0%)
s_l_e




    FALSE 201 (100%) 136 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 130 (95%) 68 (94%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 7 (5.1%) 4 (5.6%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 10 (5.0%) 16 (12%) 4 (5.6%) 6 (5.6%) 3 (3.5%)
    TRUE 191 (95%) 121 (88%) 68 (94%) 101 (94%) 82 (96%)
e_l_b




    FALSE 0 (0%) 7 (5.1%) 5 (6.9%) 2 (1.9%) 0 (0%)
    TRUE 201 (100%) 130 (95%) 67 (93%) 105 (98%) 85 (100%)
e_l_s




    FALSE 0 (0%) 6 (4.4%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 131 (96%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 192 (96%) 122 (89%) 69 (96%) 101 (94%) 83 (98%)
    TRUE 9 (4.5%) 15 (11%) 3 (4.2%) 6 (5.6%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 131 (96%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 6 (4.4%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 5

chrom <- 5
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 127 (93%) 70 (97%) 105 (98%) 83 (98%)
    TRUE 0 (0%) 10 (7.3%) 2 (2.8%) 2 (1.9%) 2 (2.4%)
b_l_s




    FALSE 2 (1.0%) 7 (5.1%) 6 (8.3%) 5 (4.7%) 1 (1.2%)
    TRUE 199 (99%) 130 (95%) 66 (92%) 102 (95%) 84 (99%)
e_l_b




    FALSE 0 (0%) 10 (7.3%) 3 (4.2%) 2 (1.9%) 2 (2.4%)
    TRUE 201 (100%) 127 (93%) 69 (96%) 105 (98%) 83 (98%)
e_l_s




    FALSE 0 (0%) 1 (0.7%) 1 (1.4%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 71 (99%) 107 (100%) 85 (100%)
s_l_b




    FALSE 199 (99%) 131 (96%) 66 (92%) 102 (95%) 84 (99%)
    TRUE 2 (1.0%) 6 (4.4%) 6 (8.3%) 5 (4.7%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 136 (99%) 71 (99%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 1 (1.4%) 0 (0%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 129 (94%) 69 (96%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 8 (5.8%) 3 (4.2%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 10 (5.0%) 9 (6.6%) 2 (2.8%) 6 (5.6%) 1 (1.2%)
    TRUE 191 (95%) 128 (93%) 70 (97%) 101 (94%) 84 (99%)
e_l_b




    FALSE 0 (0%) 8 (5.8%) 3 (4.2%) 2 (1.9%) 0 (0%)
    TRUE 201 (100%) 129 (94%) 69 (96%) 105 (98%) 85 (100%)
e_l_s




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 191 (95%) 129 (94%) 70 (97%) 101 (94%) 84 (99%)
    TRUE 10 (5.0%) 8 (5.8%) 2 (2.8%) 6 (5.6%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 6

chrom <- 6
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 118 (86%) 66 (92%) 98 (92%) 83 (98%)
    TRUE 0 (0%) 19 (14%) 6 (8.3%) 9 (8.4%) 2 (2.4%)
b_l_s




    FALSE 3 (1.5%) 9 (6.6%) 2 (2.8%) 7 (6.5%) 1 (1.2%)
    TRUE 198 (99%) 128 (93%) 70 (97%) 100 (93%) 84 (99%)
e_l_b




    FALSE 0 (0%) 19 (14%) 6 (8.3%) 9 (8.4%) 2 (2.4%)
    TRUE 201 (100%) 118 (86%) 66 (92%) 98 (92%) 83 (98%)
e_l_s




    FALSE 0 (0%) 7 (5.1%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 130 (95%) 72 (100%) 106 (99%) 85 (100%)
s_l_b




    FALSE 199 (99%) 128 (93%) 70 (97%) 102 (95%) 84 (99%)
    TRUE 2 (1.0%) 9 (6.6%) 2 (2.8%) 5 (4.7%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 131 (96%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 6 (4.4%) 0 (0%) 1 (0.9%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 127 (93%) 70 (97%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 10 (7.3%) 2 (2.8%) 2 (1.9%) 0 (0%)
b_l_s




    FALSE 6 (3.0%) 12 (8.8%) 3 (4.2%) 8 (7.5%) 2 (2.4%)
    TRUE 195 (97%) 125 (91%) 69 (96%) 99 (93%) 83 (98%)
e_l_b




    FALSE 0 (0%) 10 (7.3%) 2 (2.8%) 4 (3.7%) 0 (0%)
    TRUE 201 (100%) 127 (93%) 70 (97%) 103 (96%) 85 (100%)
e_l_s




    FALSE 0 (0%) 3 (2.2%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 134 (98%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 195 (97%) 127 (93%) 69 (96%) 100 (93%) 83 (98%)
    TRUE 6 (3.0%) 10 (7.3%) 3 (4.2%) 7 (6.5%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 134 (98%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 7

chrom <- 7
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 127 (93%) 69 (96%) 99 (93%) 84 (99%)
    TRUE 0 (0%) 10 (7.3%) 3 (4.2%) 8 (7.5%) 1 (1.2%)
b_l_s




    FALSE 6 (3.0%) 1 (0.7%) 3 (4.2%) 6 (5.6%) 1 (1.2%)
    TRUE 195 (97%) 136 (99%) 69 (96%) 101 (94%) 84 (99%)
e_l_b




    FALSE 0 (0%) 11 (8.0%) 3 (4.2%) 9 (8.4%) 1 (1.2%)
    TRUE 201 (100%) 126 (92%) 69 (96%) 98 (92%) 84 (99%)
e_l_s




    FALSE 0 (0%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
s_l_b




    FALSE 195 (97%) 136 (99%) 69 (96%) 101 (94%) 84 (99%)
    TRUE 6 (3.0%) 1 (0.7%) 3 (4.2%) 6 (5.6%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 137 (100%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 0 (0%) 0 (0%) 1 (0.9%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 200 (100%) 133 (97%) 71 (99%) 105 (98%) 83 (98%)
    TRUE 1 (0.5%) 4 (2.9%) 1 (1.4%) 2 (1.9%) 2 (2.4%)
b_l_s




    FALSE 8 (4.0%) 13 (9.5%) 5 (6.9%) 6 (5.6%) 2 (2.4%)
    TRUE 193 (96%) 124 (91%) 67 (93%) 101 (94%) 83 (98%)
e_l_b




    FALSE 1 (0.5%) 4 (2.9%) 1 (1.4%) 2 (1.9%) 2 (2.4%)
    TRUE 200 (100%) 133 (97%) 71 (99%) 105 (98%) 83 (98%)
e_l_s




    FALSE 0 (0%) 3 (2.2%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 134 (98%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 195 (97%) 124 (91%) 67 (93%) 101 (94%) 83 (98%)
    TRUE 6 (3.0%) 13 (9.5%) 5 (6.9%) 6 (5.6%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 134 (98%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 8

chrom <- 8
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 63 (31%) 35 (26%) 1 (1.4%) 20 (19%) 29 (34%)
    TRUE 138 (69%) 102 (74%) 71 (99%) 87 (81%) 56 (66%)
b_l_s




    FALSE 81 (40%) 44 (32%) 49 (68%) 41 (38%) 32 (38%)
    TRUE 120 (60%) 93 (68%) 23 (32%) 66 (62%) 53 (62%)
e_l_b




    FALSE 138 (69%) 102 (74%) 71 (99%) 87 (81%) 57 (67%)
    TRUE 63 (31%) 35 (26%) 1 (1.4%) 20 (19%) 28 (33%)
e_l_s




    FALSE 140 (70%) 100 (73%) 69 (96%) 87 (81%) 56 (66%)
    TRUE 61 (30%) 37 (27%) 3 (4.2%) 20 (19%) 29 (34%)
s_l_b




    FALSE 124 (62%) 96 (70%) 29 (40%) 68 (64%) 55 (65%)
    TRUE 77 (38%) 41 (30%) 43 (60%) 39 (36%) 30 (35%)
s_l_e




    FALSE 61 (30%) 37 (27%) 3 (4.2%) 20 (19%) 29 (34%)
    TRUE 140 (70%) 100 (73%) 69 (96%) 87 (81%) 56 (66%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 126 (92%) 70 (97%) 100 (93%) 84 (99%)
    TRUE 0 (0%) 11 (8.0%) 2 (2.8%) 7 (6.5%) 1 (1.2%)
b_l_s




    FALSE 5 (2.5%) 11 (8.0%) 13 (18%) 14 (13%) 4 (4.7%)
    TRUE 196 (98%) 126 (92%) 59 (82%) 93 (87%) 81 (95%)
e_l_b




    FALSE 0 (0%) 11 (8.0%) 2 (2.8%) 7 (6.5%) 1 (1.2%)
    TRUE 201 (100%) 126 (92%) 70 (97%) 100 (93%) 84 (99%)
e_l_s




    FALSE 0 (0%) 5 (3.6%) 2 (2.8%) 2 (1.9%) 1 (1.2%)
    TRUE 201 (100%) 132 (96%) 70 (97%) 105 (98%) 84 (99%)
s_l_b




    FALSE 196 (98%) 126 (92%) 59 (82%) 93 (87%) 81 (95%)
    TRUE 5 (2.5%) 11 (8.0%) 13 (18%) 14 (13%) 4 (4.7%)
s_l_e




    FALSE 201 (100%) 132 (96%) 70 (97%) 105 (98%) 84 (99%)
    TRUE 0 (0%) 5 (3.6%) 2 (2.8%) 2 (1.9%) 1 (1.2%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 9

chrom <- 9
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 125 (91%) 68 (94%) 98 (92%) 84 (99%)
    TRUE 0 (0%) 12 (8.8%) 4 (5.6%) 9 (8.4%) 1 (1.2%)
b_l_s




    FALSE 11 (5.5%) 7 (5.1%) 4 (5.6%) 10 (9.3%) 4 (4.7%)
    TRUE 190 (95%) 130 (95%) 68 (94%) 97 (91%) 81 (95%)
e_l_b




    FALSE 0 (0%) 14 (10%) 4 (5.6%) 10 (9.3%) 1 (1.2%)
    TRUE 201 (100%) 123 (90%) 68 (94%) 97 (91%) 84 (99%)
e_l_s




    FALSE 0 (0%) 4 (2.9%) 1 (1.4%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 133 (97%) 71 (99%) 107 (100%) 85 (100%)
s_l_b




    FALSE 191 (95%) 130 (95%) 68 (94%) 97 (91%) 82 (96%)
    TRUE 10 (5.0%) 7 (5.1%) 4 (5.6%) 10 (9.3%) 3 (3.5%)
s_l_e




    FALSE 201 (100%) 133 (97%) 71 (99%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 4 (2.9%) 1 (1.4%) 0 (0%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 128 (93%) 71 (99%) 100 (93%) 85 (100%)
    TRUE 0 (0%) 9 (6.6%) 1 (1.4%) 7 (6.5%) 0 (0%)
b_l_s




    FALSE 8 (4.0%) 8 (5.8%) 4 (5.6%) 14 (13%) 3 (3.5%)
    TRUE 193 (96%) 129 (94%) 68 (94%) 93 (87%) 82 (96%)
e_l_b




    FALSE 0 (0%) 9 (6.6%) 1 (1.4%) 8 (7.5%) 0 (0%)
    TRUE 201 (100%) 128 (93%) 71 (99%) 99 (93%) 85 (100%)
e_l_s




    FALSE 0 (0%) 4 (2.9%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 133 (97%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 193 (96%) 129 (94%) 68 (94%) 96 (90%) 82 (96%)
    TRUE 8 (4.0%) 8 (5.8%) 4 (5.6%) 11 (10%) 3 (3.5%)
s_l_e




    FALSE 201 (100%) 133 (97%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 4 (2.9%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 10

chrom <- 10
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 131 (96%) 63 (88%) 102 (95%) 81 (95%)
    TRUE 0 (0%) 6 (4.4%) 9 (13%) 5 (4.7%) 4 (4.7%)
b_l_s




    FALSE 5 (2.5%) 6 (4.4%) 5 (6.9%) 11 (10%) 1 (1.2%)
    TRUE 196 (98%) 131 (96%) 67 (93%) 96 (90%) 84 (99%)
e_l_b




    FALSE 0 (0%) 6 (4.4%) 9 (13%) 7 (6.5%) 4 (4.7%)
    TRUE 201 (100%) 131 (96%) 63 (88%) 100 (93%) 81 (95%)
e_l_s




    FALSE 0 (0%) 1 (0.7%) 2 (2.8%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 70 (97%) 107 (100%) 85 (100%)
s_l_b




    FALSE 197 (98%) 131 (96%) 67 (93%) 97 (91%) 84 (99%)
    TRUE 4 (2.0%) 6 (4.4%) 5 (6.9%) 10 (9.3%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 136 (99%) 70 (97%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 2 (2.8%) 0 (0%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 130 (95%) 68 (94%) 103 (96%) 84 (99%)
    TRUE 0 (0%) 7 (5.1%) 4 (5.6%) 4 (3.7%) 1 (1.2%)
b_l_s




    FALSE 6 (3.0%) 18 (13%) 4 (5.6%) 12 (11%) 2 (2.4%)
    TRUE 195 (97%) 119 (87%) 68 (94%) 95 (89%) 83 (98%)
e_l_b




    FALSE 0 (0%) 8 (5.8%) 5 (6.9%) 4 (3.7%) 2 (2.4%)
    TRUE 201 (100%) 129 (94%) 67 (93%) 103 (96%) 83 (98%)
e_l_s




    FALSE 0 (0%) 1 (0.7%) 1 (1.4%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 136 (99%) 71 (99%) 107 (100%) 85 (100%)
s_l_b




    FALSE 196 (98%) 120 (88%) 68 (94%) 96 (90%) 83 (98%)
    TRUE 5 (2.5%) 17 (12%) 4 (5.6%) 11 (10%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 136 (99%) 71 (99%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 1 (1.4%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 11

chrom <- 11
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 124 (91%) 68 (94%) 101 (94%) 84 (99%)
    TRUE 0 (0%) 13 (9.5%) 4 (5.6%) 6 (5.6%) 1 (1.2%)
b_l_s




    FALSE 8 (4.0%) 13 (9.5%) 8 (11%) 16 (15%) 2 (2.4%)
    TRUE 193 (96%) 124 (91%) 64 (89%) 91 (85%) 83 (98%)
e_l_b




    FALSE 0 (0%) 14 (10%) 5 (6.9%) 6 (5.6%) 1 (1.2%)
    TRUE 201 (100%) 123 (90%) 67 (93%) 101 (94%) 84 (99%)
e_l_s




    FALSE 0 (0%) 6 (4.4%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 131 (96%) 72 (100%) 106 (99%) 85 (100%)
s_l_b




    FALSE 195 (97%) 125 (91%) 66 (92%) 91 (85%) 83 (98%)
    TRUE 6 (3.0%) 12 (8.8%) 6 (8.3%) 16 (15%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 132 (96%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 5 (3.6%) 0 (0%) 1 (0.9%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 125 (91%) 71 (99%) 101 (94%) 85 (100%)
    TRUE 0 (0%) 12 (8.8%) 1 (1.4%) 6 (5.6%) 0 (0%)
b_l_s




    FALSE 4 (2.0%) 13 (9.5%) 4 (5.6%) 9 (8.4%) 2 (2.4%)
    TRUE 197 (98%) 124 (91%) 68 (94%) 98 (92%) 83 (98%)
e_l_b




    FALSE 0 (0%) 12 (8.8%) 1 (1.4%) 6 (5.6%) 0 (0%)
    TRUE 201 (100%) 125 (91%) 71 (99%) 101 (94%) 85 (100%)
e_l_s




    FALSE 0 (0%) 5 (3.6%) 1 (1.4%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 132 (96%) 71 (99%) 107 (100%) 85 (100%)
s_l_b




    FALSE 197 (98%) 124 (91%) 68 (94%) 99 (93%) 84 (99%)
    TRUE 4 (2.0%) 13 (9.5%) 4 (5.6%) 8 (7.5%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 133 (97%) 71 (99%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 4 (2.9%) 1 (1.4%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 12

chrom <- 12
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 126 (92%) 67 (93%) 103 (96%) 83 (98%)
    TRUE 0 (0%) 11 (8.0%) 5 (6.9%) 4 (3.7%) 2 (2.4%)
b_l_s




    FALSE 13 (6.5%) 13 (9.5%) 6 (8.3%) 7 (6.5%) 4 (4.7%)
    TRUE 188 (94%) 124 (91%) 66 (92%) 100 (93%) 81 (95%)
e_l_b




    FALSE 0 (0%) 12 (8.8%) 5 (6.9%) 4 (3.7%) 2 (2.4%)
    TRUE 201 (100%) 125 (91%) 67 (93%) 103 (96%) 83 (98%)
e_l_s




    TRUE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 188 (94%) 125 (91%) 68 (94%) 101 (94%) 82 (96%)
    TRUE 13 (6.5%) 12 (8.8%) 4 (5.6%) 6 (5.6%) 3 (3.5%)
s_l_e




    FALSE 201 (100%) 137 (100%) 72 (100%) 107 (100%) 85 (100%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 131 (96%) 69 (96%) 104 (97%) 83 (98%)
    TRUE 0 (0%) 6 (4.4%) 3 (4.2%) 3 (2.8%) 2 (2.4%)
b_l_s




    FALSE 3 (1.5%) 13 (9.5%) 8 (11%) 9 (8.4%) 1 (1.2%)
    TRUE 198 (99%) 124 (91%) 64 (89%) 98 (92%) 84 (99%)
e_l_b




    FALSE 0 (0%) 6 (4.4%) 3 (4.2%) 3 (2.8%) 2 (2.4%)
    TRUE 201 (100%) 131 (96%) 69 (96%) 104 (97%) 83 (98%)
e_l_s




    FALSE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 198 (99%) 125 (91%) 64 (89%) 99 (93%) 84 (99%)
    TRUE 3 (1.5%) 12 (8.8%) 8 (11%) 8 (7.5%) 1 (1.2%)
s_l_e




    FALSE 201 (100%) 135 (99%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 13

chrom <- 13
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 200 (100%) 121 (88%) 69 (96%) 101 (94%) 84 (99%)
    TRUE 1 (0.5%) 16 (12%) 3 (4.2%) 6 (5.6%) 1 (1.2%)
b_l_s




    FALSE 14 (7.0%) 11 (8.0%) 9 (13%) 11 (10%) 4 (4.7%)
    TRUE 187 (93%) 126 (92%) 63 (88%) 96 (90%) 81 (95%)
e_l_b




    FALSE 1 (0.5%) 18 (13%) 4 (5.6%) 6 (5.6%) 1 (1.2%)
    TRUE 200 (100%) 119 (87%) 68 (94%) 101 (94%) 84 (99%)
e_l_s




    FALSE 0 (0%) 4 (2.9%) 2 (2.8%) 0 (0%) 1 (1.2%)
    TRUE 201 (100%) 133 (97%) 70 (97%) 107 (100%) 84 (99%)
s_l_b




    FALSE 187 (93%) 127 (93%) 63 (88%) 98 (92%) 83 (98%)
    TRUE 14 (7.0%) 10 (7.3%) 9 (13%) 9 (8.4%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 133 (97%) 70 (97%) 107 (100%) 84 (99%)
    TRUE 0 (0%) 4 (2.9%) 2 (2.8%) 0 (0%) 1 (1.2%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 200 (100%) 129 (94%) 68 (94%) 96 (90%) 76 (89%)
    TRUE 1 (0.5%) 8 (5.8%) 4 (5.6%) 11 (10%) 9 (11%)
b_l_s




    FALSE 11 (5.5%) 11 (8.0%) 9 (13%) 18 (17%) 5 (5.9%)
    TRUE 190 (95%) 126 (92%) 63 (88%) 89 (83%) 80 (94%)
e_l_b




    FALSE 1 (0.5%) 9 (6.6%) 4 (5.6%) 11 (10%) 9 (11%)
    TRUE 200 (100%) 128 (93%) 68 (94%) 96 (90%) 76 (89%)
e_l_s




    FALSE 0 (0%) 4 (2.9%) 1 (1.4%) 1 (0.9%) 1 (1.2%)
    TRUE 201 (100%) 133 (97%) 71 (99%) 106 (99%) 84 (99%)
s_l_b




    FALSE 190 (95%) 127 (93%) 64 (89%) 90 (84%) 80 (94%)
    TRUE 11 (5.5%) 10 (7.3%) 8 (11%) 17 (16%) 5 (5.9%)
s_l_e




    FALSE 201 (100%) 134 (98%) 72 (100%) 106 (99%) 84 (99%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 1 (0.9%) 1 (1.2%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 14

chrom <- 14
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 200 (100%) 115 (84%) 59 (82%) 90 (84%) 82 (96%)
    TRUE 1 (0.5%) 22 (16%) 13 (18%) 17 (16%) 3 (3.5%)
b_l_s




    FALSE 9 (4.5%) 16 (12%) 8 (11%) 16 (15%) 6 (7.1%)
    TRUE 192 (96%) 121 (88%) 64 (89%) 91 (85%) 79 (93%)
e_l_b




    FALSE 1 (0.5%) 22 (16%) 13 (18%) 18 (17%) 4 (4.7%)
    TRUE 200 (100%) 115 (84%) 59 (82%) 89 (83%) 81 (95%)
e_l_s




    FALSE 0 (0%) 3 (2.2%) 1 (1.4%) 4 (3.7%) 0 (0%)
    TRUE 201 (100%) 134 (98%) 71 (99%) 103 (96%) 85 (100%)
s_l_b




    FALSE 193 (96%) 122 (89%) 64 (89%) 91 (85%) 79 (93%)
    TRUE 8 (4.0%) 15 (11%) 8 (11%) 16 (15%) 6 (7.1%)
s_l_e




    FALSE 201 (100%) 134 (98%) 71 (99%) 103 (96%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 1 (1.4%) 4 (3.7%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 122 (89%) 64 (89%) 98 (92%) 83 (98%)
    TRUE 0 (0%) 15 (11%) 8 (11%) 9 (8.4%) 2 (2.4%)
b_l_s




    FALSE 7 (3.5%) 12 (8.8%) 9 (13%) 13 (12%) 5 (5.9%)
    TRUE 194 (97%) 125 (91%) 63 (88%) 94 (88%) 80 (94%)
e_l_b




    FALSE 0 (0%) 16 (12%) 8 (11%) 12 (11%) 2 (2.4%)
    TRUE 201 (100%) 121 (88%) 64 (89%) 95 (89%) 83 (98%)
e_l_s




    FALSE 0 (0%) 2 (1.5%) 1 (1.4%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 135 (99%) 71 (99%) 106 (99%) 85 (100%)
s_l_b




    FALSE 194 (97%) 125 (91%) 63 (88%) 96 (90%) 80 (94%)
    TRUE 7 (3.5%) 12 (8.8%) 9 (13%) 11 (10%) 5 (5.9%)
s_l_e




    FALSE 201 (100%) 135 (99%) 71 (99%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 2 (1.5%) 1 (1.4%) 1 (0.9%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 15

chrom <- 15
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 194 (97%) 122 (89%) 65 (90%) 90 (84%) 81 (95%)
    TRUE 7 (3.5%) 15 (11%) 7 (9.7%) 17 (16%) 4 (4.7%)
b_l_s




    FALSE 11 (5.5%) 14 (10%) 8 (11%) 19 (18%) 3 (3.5%)
    TRUE 190 (95%) 123 (90%) 64 (89%) 88 (82%) 82 (96%)
e_l_b




    FALSE 7 (3.5%) 17 (12%) 8 (11%) 18 (17%) 5 (5.9%)
    TRUE 194 (97%) 120 (88%) 64 (89%) 89 (83%) 80 (94%)
e_l_s




    FALSE 0 (0%) 5 (3.6%) 0 (0%) 3 (2.8%) 0 (0%)
    TRUE 201 (100%) 132 (96%) 72 (100%) 104 (97%) 85 (100%)
s_l_b




    FALSE 192 (96%) 124 (91%) 67 (93%) 90 (84%) 83 (98%)
    TRUE 9 (4.5%) 13 (9.5%) 5 (6.9%) 17 (16%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 133 (97%) 72 (100%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 4 (2.9%) 0 (0%) 2 (1.9%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 196 (98%) 129 (94%) 66 (92%) 100 (93%) 80 (94%)
    TRUE 5 (2.5%) 8 (5.8%) 6 (8.3%) 7 (6.5%) 5 (5.9%)
b_l_s




    FALSE 12 (6.0%) 15 (11%) 8 (11%) 21 (20%) 0 (0%)
    TRUE 189 (94%) 122 (89%) 64 (89%) 86 (80%) 85 (100%)
e_l_b




    FALSE 5 (2.5%) 12 (8.8%) 7 (9.7%) 8 (7.5%) 5 (5.9%)
    TRUE 196 (98%) 125 (91%) 65 (90%) 99 (93%) 80 (94%)
e_l_s




    FALSE 2 (1.0%) 4 (2.9%) 0 (0%) 3 (2.8%) 0 (0%)
    TRUE 199 (99%) 133 (97%) 72 (100%) 104 (97%) 85 (100%)
s_l_b




    FALSE 191 (95%) 125 (91%) 64 (89%) 87 (81%) 85 (100%)
    TRUE 10 (5.0%) 12 (8.8%) 8 (11%) 20 (19%) 0 (0%)
s_l_e




    FALSE 200 (100%) 133 (97%) 72 (100%) 104 (97%) 85 (100%)
    TRUE 1 (0.5%) 4 (2.9%) 0 (0%) 3 (2.8%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 16

chrom <- 16
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 128 (93%) 68 (94%) 100 (93%) 85 (100%)
    TRUE 0 (0%) 9 (6.6%) 4 (5.6%) 7 (6.5%) 0 (0%)
b_l_s




    FALSE 6 (3.0%) 13 (9.5%) 7 (9.7%) 8 (7.5%) 4 (4.7%)
    TRUE 195 (97%) 124 (91%) 65 (90%) 99 (93%) 81 (95%)
e_l_b




    FALSE 0 (0%) 10 (7.3%) 5 (6.9%) 7 (6.5%) 0 (0%)
    TRUE 201 (100%) 127 (93%) 67 (93%) 100 (93%) 85 (100%)
e_l_s




    FALSE 0 (0%) 2 (1.5%) 0 (0%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 135 (99%) 72 (100%) 106 (99%) 85 (100%)
s_l_b




    FALSE 195 (97%) 124 (91%) 66 (92%) 99 (93%) 81 (95%)
    TRUE 6 (3.0%) 13 (9.5%) 6 (8.3%) 8 (7.5%) 4 (4.7%)
s_l_e




    FALSE 201 (100%) 135 (99%) 72 (100%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 2 (1.5%) 0 (0%) 1 (0.9%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 128 (93%) 70 (97%) 92 (86%) 82 (96%)
    TRUE 0 (0%) 9 (6.6%) 2 (2.8%) 15 (14%) 3 (3.5%)
b_l_s




    FALSE 10 (5.0%) 13 (9.5%) 15 (21%) 12 (11%) 9 (11%)
    TRUE 191 (95%) 124 (91%) 57 (79%) 95 (89%) 76 (89%)
e_l_b




    FALSE 0 (0%) 9 (6.6%) 2 (2.8%) 16 (15%) 3 (3.5%)
    TRUE 201 (100%) 128 (93%) 70 (97%) 91 (85%) 82 (96%)
e_l_s




    FALSE 3 (1.5%) 1 (0.7%) 1 (1.4%) 1 (0.9%) 2 (2.4%)
    TRUE 198 (99%) 136 (99%) 71 (99%) 106 (99%) 83 (98%)
s_l_b




    FALSE 192 (96%) 126 (92%) 59 (82%) 96 (90%) 76 (89%)
    TRUE 9 (4.5%) 11 (8.0%) 13 (18%) 11 (10%) 9 (11%)
s_l_e




    FALSE 198 (99%) 137 (100%) 71 (99%) 106 (99%) 83 (98%)
    TRUE 3 (1.5%) 0 (0%) 1 (1.4%) 1 (0.9%) 2 (2.4%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 17

chrom <- 17
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 200 (100%) 125 (91%) 66 (92%) 89 (83%) 79 (93%)
    TRUE 1 (0.5%) 12 (8.8%) 6 (8.3%) 18 (17%) 6 (7.1%)
b_l_s




    FALSE 10 (5.0%) 15 (11%) 9 (13%) 18 (17%) 5 (5.9%)
    TRUE 191 (95%) 122 (89%) 63 (88%) 89 (83%) 80 (94%)
e_l_b




    FALSE 2 (1.0%) 14 (10%) 6 (8.3%) 21 (20%) 6 (7.1%)
    TRUE 199 (99%) 123 (90%) 66 (92%) 86 (80%) 79 (93%)
e_l_s




    FALSE 0 (0%) 3 (2.2%) 0 (0%) 0 (0%) 0 (0%)
    TRUE 201 (100%) 134 (98%) 72 (100%) 107 (100%) 85 (100%)
s_l_b




    FALSE 192 (96%) 122 (89%) 63 (88%) 90 (84%) 81 (95%)
    TRUE 9 (4.5%) 15 (11%) 9 (13%) 17 (16%) 4 (4.7%)
s_l_e




    FALSE 201 (100%) 134 (98%) 72 (100%) 107 (100%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 0 (0%) 0 (0%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 183 (91%) 128 (93%) 67 (93%) 99 (93%) 82 (96%)
    TRUE 18 (9.0%) 9 (6.6%) 5 (6.9%) 8 (7.5%) 3 (3.5%)
b_l_s




    FALSE 14 (7.0%) 12 (8.8%) 13 (18%) 20 (19%) 5 (5.9%)
    TRUE 187 (93%) 125 (91%) 59 (82%) 87 (81%) 80 (94%)
e_l_b




    FALSE 18 (9.0%) 9 (6.6%) 5 (6.9%) 8 (7.5%) 3 (3.5%)
    TRUE 183 (91%) 128 (93%) 67 (93%) 99 (93%) 82 (96%)
e_l_s




    FALSE 0 (0%) 2 (1.5%) 1 (1.4%) 1 (0.9%) 0 (0%)
    TRUE 201 (100%) 135 (99%) 71 (99%) 106 (99%) 85 (100%)
s_l_b




    FALSE 189 (94%) 125 (91%) 59 (82%) 91 (85%) 80 (94%)
    TRUE 12 (6.0%) 12 (8.8%) 13 (18%) 16 (15%) 5 (5.9%)
s_l_e




    FALSE 201 (100%) 136 (99%) 71 (99%) 106 (99%) 85 (100%)
    TRUE 0 (0%) 1 (0.7%) 1 (1.4%) 1 (0.9%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 18

chrom <- 18
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 200 (100%) 120 (88%) 64 (89%) 93 (87%) 78 (92%)
    TRUE 1 (0.5%) 17 (12%) 8 (11%) 14 (13%) 7 (8.2%)
b_l_s




    FALSE 16 (8.0%) 17 (12%) 9 (13%) 22 (21%) 3 (3.5%)
    TRUE 185 (92%) 120 (88%) 63 (88%) 85 (79%) 82 (96%)
e_l_b




    FALSE 1 (0.5%) 17 (12%) 8 (11%) 14 (13%) 7 (8.2%)
    TRUE 200 (100%) 120 (88%) 64 (89%) 93 (87%) 78 (92%)
e_l_s




    FALSE 0 (0%) 3 (2.2%) 3 (4.2%) 3 (2.8%) 0 (0%)
    TRUE 201 (100%) 134 (98%) 69 (96%) 104 (97%) 85 (100%)
s_l_b




    FALSE 185 (92%) 120 (88%) 63 (88%) 87 (81%) 83 (98%)
    TRUE 16 (8.0%) 17 (12%) 9 (13%) 20 (19%) 2 (2.4%)
s_l_e




    FALSE 201 (100%) 134 (98%) 69 (96%) 104 (97%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 3 (4.2%) 3 (2.8%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 199 (99%) 126 (92%) 68 (94%) 95 (89%) 81 (95%)
    TRUE 2 (1.0%) 11 (8.0%) 4 (5.6%) 12 (11%) 4 (4.7%)
b_l_s




    FALSE 6 (3.0%) 14 (10%) 11 (15%) 19 (18%) 9 (11%)
    TRUE 195 (97%) 123 (90%) 61 (85%) 88 (82%) 76 (89%)
e_l_b




    FALSE 2 (1.0%) 12 (8.8%) 5 (6.9%) 14 (13%) 4 (4.7%)
    TRUE 199 (99%) 125 (91%) 67 (93%) 93 (87%) 81 (95%)
e_l_s




    FALSE 0 (0%) 0 (0%) 1 (1.4%) 1 (0.9%) 1 (1.2%)
    TRUE 201 (100%) 137 (100%) 71 (99%) 106 (99%) 84 (99%)
s_l_b




    FALSE 195 (97%) 125 (91%) 62 (86%) 88 (82%) 76 (89%)
    TRUE 6 (3.0%) 12 (8.8%) 10 (14%) 19 (18%) 9 (11%)
s_l_e




    FALSE 201 (100%) 137 (100%) 71 (99%) 106 (99%) 84 (99%)
    TRUE 0 (0%) 0 (0%) 1 (1.4%) 1 (0.9%) 1 (1.2%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 19

chrom <- 19
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 199 (99%) 113 (82%) 61 (85%) 93 (87%) 82 (96%)
    TRUE 2 (1.0%) 24 (18%) 11 (15%) 14 (13%) 3 (3.5%)
b_l_s




    FALSE 20 (10.0%) 12 (8.8%) 12 (17%) 23 (21%) 5 (5.9%)
    TRUE 181 (90%) 125 (91%) 60 (83%) 84 (79%) 80 (94%)
e_l_b




    FALSE 2 (1.0%) 25 (18%) 11 (15%) 16 (15%) 4 (4.7%)
    TRUE 199 (99%) 112 (82%) 61 (85%) 91 (85%) 81 (95%)
e_l_s




    FALSE 0 (0%) 4 (2.9%) 3 (4.2%) 5 (4.7%) 0 (0%)
    TRUE 201 (100%) 133 (97%) 69 (96%) 102 (95%) 85 (100%)
s_l_b




    FALSE 182 (91%) 127 (93%) 62 (86%) 86 (80%) 80 (94%)
    TRUE 19 (9.5%) 10 (7.3%) 10 (14%) 21 (20%) 5 (5.9%)
s_l_e




    FALSE 201 (100%) 133 (97%) 69 (96%) 103 (96%) 85 (100%)
    TRUE 0 (0%) 4 (2.9%) 3 (4.2%) 4 (3.7%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 198 (99%) 127 (93%) 64 (89%) 93 (87%) 81 (95%)
    TRUE 3 (1.5%) 10 (7.3%) 8 (11%) 14 (13%) 4 (4.7%)
b_l_s




    FALSE 22 (11%) 17 (12%) 15 (21%) 24 (22%) 5 (5.9%)
    TRUE 179 (89%) 120 (88%) 57 (79%) 83 (78%) 80 (94%)
e_l_b




    FALSE 3 (1.5%) 12 (8.8%) 9 (13%) 14 (13%) 4 (4.7%)
    TRUE 198 (99%) 125 (91%) 63 (88%) 93 (87%) 81 (95%)
e_l_s




    FALSE 0 (0%) 4 (2.9%) 2 (2.8%) 4 (3.7%) 0 (0%)
    TRUE 201 (100%) 133 (97%) 70 (97%) 103 (96%) 85 (100%)
s_l_b




    FALSE 180 (90%) 123 (90%) 58 (81%) 85 (79%) 82 (96%)
    TRUE 21 (10%) 14 (10%) 14 (19%) 22 (21%) 3 (3.5%)
s_l_e




    FALSE 201 (100%) 133 (97%) 70 (97%) 104 (97%) 85 (100%)
    TRUE 0 (0%) 4 (2.9%) 2 (2.8%) 3 (2.8%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 20

chrom <- 20
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 201 (100%) 126 (92%) 62 (86%) 91 (85%) 81 (95%)
    TRUE 0 (0%) 11 (8.0%) 10 (14%) 16 (15%) 4 (4.7%)
b_l_s




    FALSE 28 (14%) 23 (17%) 8 (11%) 10 (9.3%) 12 (14%)
    TRUE 173 (86%) 114 (83%) 64 (89%) 97 (91%) 73 (86%)
e_l_b




    FALSE 0 (0%) 11 (8.0%) 12 (17%) 17 (16%) 4 (4.7%)
    TRUE 201 (100%) 126 (92%) 60 (83%) 90 (84%) 81 (95%)
e_l_s




    FALSE 0 (0%) 6 (4.4%) 1 (1.4%) 2 (1.9%) 0 (0%)
    TRUE 201 (100%) 131 (96%) 71 (99%) 105 (98%) 85 (100%)
s_l_b




    FALSE 175 (87%) 114 (83%) 64 (89%) 98 (92%) 74 (87%)
    TRUE 26 (13%) 23 (17%) 8 (11%) 9 (8.4%) 11 (13%)
s_l_e




    FALSE 201 (100%) 131 (96%) 71 (99%) 105 (98%) 85 (100%)
    TRUE 0 (0%) 6 (4.4%) 1 (1.4%) 2 (1.9%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 198 (99%) 121 (88%) 62 (86%) 89 (83%) 84 (99%)
    TRUE 3 (1.5%) 16 (12%) 10 (14%) 18 (17%) 1 (1.2%)
b_l_s




    FALSE 24 (12%) 21 (15%) 8 (11%) 20 (19%) 7 (8.2%)
    TRUE 177 (88%) 116 (85%) 64 (89%) 87 (81%) 78 (92%)
e_l_b




    FALSE 3 (1.5%) 16 (12%) 10 (14%) 19 (18%) 2 (2.4%)
    TRUE 198 (99%) 121 (88%) 62 (86%) 88 (82%) 83 (98%)
e_l_s




    FALSE 0 (0%) 4 (2.9%) 2 (2.8%) 4 (3.7%) 0 (0%)
    TRUE 201 (100%) 133 (97%) 70 (97%) 103 (96%) 85 (100%)
s_l_b




    FALSE 179 (89%) 117 (85%) 64 (89%) 88 (82%) 78 (92%)
    TRUE 22 (11%) 20 (15%) 8 (11%) 19 (18%) 7 (8.2%)
s_l_e




    FALSE 201 (100%) 134 (98%) 70 (97%) 103 (96%) 85 (100%)
    TRUE 0 (0%) 3 (2.2%) 2 (2.8%) 4 (3.7%) 0 (0%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 21

chrom <- 21
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 187 (93%) 97 (71%) 56 (78%) 76 (71%) 69 (81%)
    TRUE 14 (7.0%) 40 (29%) 16 (22%) 31 (29%) 16 (19%)
b_l_s




    FALSE 26 (13%) 19 (14%) 17 (24%) 19 (18%) 8 (9.4%)
    TRUE 175 (87%) 118 (86%) 55 (76%) 88 (82%) 77 (91%)
e_l_b




    FALSE 15 (7.5%) 43 (31%) 19 (26%) 32 (30%) 17 (20%)
    TRUE 186 (93%) 94 (69%) 53 (74%) 75 (70%) 68 (80%)
e_l_s




    FALSE 4 (2.0%) 13 (9.5%) 9 (13%) 13 (12%) 1 (1.2%)
    TRUE 197 (98%) 124 (91%) 63 (88%) 94 (88%) 84 (99%)
s_l_b




    FALSE 177 (88%) 122 (89%) 55 (76%) 92 (86%) 77 (91%)
    TRUE 24 (12%) 15 (11%) 17 (24%) 15 (14%) 8 (9.4%)
s_l_e




    FALSE 198 (99%) 125 (91%) 65 (90%) 95 (89%) 85 (100%)
    TRUE 3 (1.5%) 12 (8.8%) 7 (9.7%) 12 (11%) 0 (0%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 193 (96%) 105 (77%) 60 (83%) 84 (79%) 73 (86%)
    TRUE 8 (4.0%) 32 (23%) 12 (17%) 23 (21%) 12 (14%)
b_l_s




    FALSE 29 (14%) 24 (18%) 17 (24%) 20 (19%) 13 (15%)
    TRUE 172 (86%) 113 (82%) 55 (76%) 87 (81%) 72 (85%)
e_l_b




    FALSE 10 (5.0%) 37 (27%) 12 (17%) 26 (24%) 13 (15%)
    TRUE 191 (95%) 100 (73%) 60 (83%) 81 (76%) 72 (85%)
e_l_s




    FALSE 1 (0.5%) 16 (12%) 3 (4.2%) 5 (4.7%) 3 (3.5%)
    TRUE 200 (100%) 121 (88%) 69 (96%) 102 (95%) 82 (96%)
s_l_b




    FALSE 178 (89%) 113 (82%) 57 (79%) 87 (81%) 73 (86%)
    TRUE 23 (11%) 24 (18%) 15 (21%) 20 (19%) 12 (14%)
s_l_e




    FALSE 200 (100%) 122 (89%) 69 (96%) 102 (95%) 82 (96%)
    TRUE 1 (0.5%) 15 (11%) 3 (4.2%) 5 (4.7%) 3 (3.5%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_flip(df_switch_trio[[chrom]], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 184 (92%) 109 (80%) 48 (67%) 76 (71%) 65 (76%)
    TRUE 17 (8.5%) 28 (20%) 24 (33%) 31 (29%) 20 (24%)
b_l_s




    FALSE 27 (13%) 21 (15%) 15 (21%) 18 (17%) 17 (20%)
    TRUE 174 (87%) 116 (85%) 57 (79%) 89 (83%) 68 (80%)
e_l_b




    FALSE 18 (9.0%) 34 (25%) 25 (35%) 37 (35%) 22 (26%)
    TRUE 183 (91%) 103 (75%) 47 (65%) 70 (65%) 63 (74%)
e_l_s




    FALSE 2 (1.0%) 18 (13%) 5 (6.9%) 12 (11%) 3 (3.5%)
    TRUE 199 (99%) 119 (87%) 67 (93%) 95 (89%) 82 (96%)
s_l_b




    FALSE 178 (89%) 117 (85%) 59 (82%) 91 (85%) 68 (80%)
    TRUE 23 (11%) 20 (15%) 13 (18%) 16 (15%) 17 (20%)
s_l_e




    FALSE 199 (99%) 124 (91%) 67 (93%) 96 (90%) 82 (96%)
    TRUE 2 (1.0%) 13 (9.5%) 5 (6.9%) 11 (10%) 3 (3.5%)
1 n (%)
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
Characteristic AFR
N = 201
1
AMR
N = 137
1
EAS
N = 72
1
EUR
N = 107
1
SAS
N = 85
1
b_l_e




    FALSE 190 (95%) 108 (79%) 59 (82%) 81 (76%) 72 (85%)
    TRUE 11 (5.5%) 29 (21%) 13 (18%) 26 (24%) 13 (15%)
b_l_s




    FALSE 25 (12%) 20 (15%) 16 (22%) 20 (19%) 9 (11%)
    TRUE 176 (88%) 117 (85%) 56 (78%) 87 (81%) 76 (89%)
e_l_b




    FALSE 14 (7.0%) 31 (23%) 16 (22%) 30 (28%) 15 (18%)
    TRUE 187 (93%) 106 (77%) 56 (78%) 77 (72%) 70 (82%)
e_l_s




    FALSE 1 (0.5%) 16 (12%) 6 (8.3%) 10 (9.3%) 2 (2.4%)
    TRUE 200 (100%) 121 (88%) 66 (92%) 97 (91%) 83 (98%)
s_l_b




    FALSE 178 (89%) 119 (87%) 56 (78%) 89 (83%) 76 (89%)
    TRUE 23 (11%) 18 (13%) 16 (22%) 18 (17%) 9 (11%)
s_l_e




    FALSE 200 (100%) 122 (89%) 66 (92%) 100 (93%) 84 (99%)
    TRUE 1 (0.5%) 15 (11%) 6 (8.3%) 7 (6.5%) 1 (1.2%)
1 n (%)
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Chromosome X

plot_flips(df_switch_x, "Beagle", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flips(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
table_flip(df_switch_x, "pop")
Characteristic AFR
N = 200
1
AMR
N = 200
1
EAS
N = 200
1
EUR
N = 200
1
SAS
N = 200
1
b_l_e




    FALSE 120 (60%) 107 (54%) 115 (58%) 112 (56%) 94 (47%)
    TRUE 80 (40%) 93 (47%) 85 (43%) 88 (44%) 106 (53%)
b_l_s




    FALSE 13 (6.5%) 29 (15%) 41 (21%) 21 (11%) 26 (13%)
    TRUE 187 (94%) 171 (86%) 159 (80%) 179 (90%) 174 (87%)
e_l_b




    FALSE 86 (43%) 105 (53%) 93 (47%) 95 (48%) 114 (57%)
    TRUE 114 (57%) 95 (48%) 107 (54%) 105 (53%) 86 (43%)
e_l_s




    FALSE 14 (7.0%) 30 (15%) 55 (28%) 37 (19%) 42 (21%)
    TRUE 186 (93%) 170 (85%) 145 (73%) 163 (82%) 158 (79%)
s_l_b




    FALSE 191 (96%) 174 (87%) 163 (82%) 180 (90%) 177 (89%)
    TRUE 9 (4.5%) 26 (13%) 37 (19%) 20 (10%) 23 (12%)
s_l_e




    FALSE 188 (94%) 171 (86%) 151 (76%) 167 (84%) 160 (80%)
    TRUE 12 (6.0%) 29 (15%) 49 (25%) 33 (17%) 40 (20%)
1 n (%)
cross_meth_plot(df_switch_x, "Flips", plot_flips, "pop", "X")

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19

Flip Rate

plot_flip_rate <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_beagle / n_hets,
         Eagle = n_flip_eagle / n_hets,
         SHAPEIT = n_flip_shapeit / n_hets) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Flip rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_flip_rate_noth <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_b / n_het,
         Eagle = n_flip_e / n_het,
         SHAPEIT = n_flip_s / n_het) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Flip rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

Chromosome 1

chrom <- 1

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 2

chrom <- 2

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 3

chrom <- 3

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 4

chrom <- 4

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 5

chrom <- 5

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 6

chrom <- 6

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 7

chrom <- 7

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 8

chrom <- 8

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 9

chrom <- 9

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 10

chrom <- 10

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 11

chrom <- 11

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 12

chrom <- 12

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 13

chrom <- 13

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 14

chrom <- 14

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 15

chrom <- 15

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 16

chrom <- 16

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 17

chrom <- 17

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 18

chrom <- 18

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
b3306a4 theandyb 2025-06-19
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 19

chrom <- 19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 20

chrom <- 20

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Version Author Date
9548985 theandyb 2025-07-14

Chromosome 21

chrom <- 21

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Version Author Date
9548985 theandyb 2025-07-14
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Chromosome X

plot_flip_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_flip_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_flip_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

cross_meth_plot(df_switch_x, "Flips", plot_flip_rate, "pop", "X")


sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] gridExtra_2.3   gtsummary_2.1.0 yaml_2.3.10     reactable_0.4.4
 [5] pander_0.6.6    lubridate_1.9.4 forcats_1.0.0   stringr_1.5.1  
 [9] dplyr_1.1.4     purrr_1.0.4     readr_2.1.5     tidyr_1.3.1    
[13] tibble_3.2.1    ggplot2_3.5.2   tidyverse_2.0.0 workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] Rdpack_2.6.3        sandwich_3.1-1      rlang_1.1.5        
 [4] magrittr_2.0.3      git2r_0.33.0        multcomp_1.4-28    
 [7] compiler_4.5.1      getPass_0.2-4       callr_3.7.6        
[10] vctrs_0.6.5         pkgconfig_2.0.3     crayon_1.5.3       
[13] fastmap_1.2.0       backports_1.5.0     labeling_0.4.3     
[16] utf8_1.2.4          promises_1.3.2      rmarkdown_2.29     
[19] markdown_2.0        tzdb_0.5.0          ps_1.9.0           
[22] nloptr_2.2.1        bit_4.6.0           xfun_0.52          
[25] cachem_1.1.0        litedown_0.7        jsonlite_1.9.1     
[28] later_1.4.1         broom_1.0.7         parallel_4.5.1     
[31] R6_2.6.1            bslib_0.9.0         stringi_1.8.4      
[34] RColorBrewer_1.1-3  boot_1.3-31         jquerylib_0.1.4    
[37] numDeriv_2016.8-1.1 estimability_1.5.1  Rcpp_1.0.14        
[40] knitr_1.50          zoo_1.8-13          httpuv_1.6.15      
[43] Matrix_1.7-3        splines_4.5.1       timechange_0.3.0   
[46] tidyselect_1.2.1    rstudioapi_0.17.1   codetools_0.2-20   
[49] processx_3.8.6      lattice_0.22-6      lmerTest_3.1-3     
[52] withr_3.0.2         coda_0.19-4.1       evaluate_1.0.3     
[55] archive_1.1.12      survival_3.8-3      xml2_1.3.8         
[58] pillar_1.10.1       whisker_0.4.1       reformulas_0.4.1   
[61] generics_0.1.3      vroom_1.6.5         rprojroot_2.0.4    
[64] hms_1.1.3           commonmark_1.9.5    munsell_0.5.1      
[67] scales_1.3.0        minqa_1.2.8         xtable_1.8-4       
[70] glue_1.8.0          emmeans_1.11.0      tools_4.5.1        
[73] lme4_1.1-36         fs_1.6.5            mvtnorm_1.3-3      
[76] cowplot_1.1.3       rbibutils_2.3       crosstalk_1.2.1    
[79] cards_0.5.1         colorspace_2.1-1    nlme_3.1-167       
[82] cli_3.6.4           gt_0.11.1           gtable_0.3.6       
[85] reactR_0.6.1        sass_0.4.10         digest_0.6.37      
[88] pbkrtest_0.5.3      TH.data_1.1-3       htmlwidgets_1.6.4  
[91] farver_2.1.2        htmltools_0.5.8.1   lifecycle_1.0.4    
[94] httr_1.4.7          bit64_4.6.0-1       MASS_7.3-65